├── Data ├── Motifs │ └── pwms_all_motifs │ │ ├── M249_0.6.txt │ │ ├── M255_0.6.txt │ │ ├── M259_0.6.txt │ │ ├── M263_0.6.txt │ │ ├── M264_0.6.txt │ │ ├── M265_0.6.txt │ │ ├── M266_0.6.txt │ │ ├── M267_0.6.txt │ │ ├── M268_0.6.txt │ │ ├── M270_0.6.txt │ │ ├── M280_0.6.txt │ │ ├── M281_0.6.txt │ │ ├── M283_0.6.txt │ │ ├── M284_0.6.txt │ │ ├── M285_0.6.txt │ │ ├── M293_0.6.txt │ │ ├── M294_0.6.txt │ │ ├── M295_0.6.txt │ │ ├── M301_0.6.txt │ │ ├── M302_0.6.txt │ │ ├── M303_0.6.txt │ │ ├── M304_0.6.txt │ │ ├── M305_0.6.txt │ │ ├── M308_0.6.txt │ │ ├── M309_0.6.txt │ │ ├── M310_0.6.txt │ │ ├── M311_0.6.txt │ │ ├── M312_0.6.txt │ │ ├── M313_0.6.txt │ │ ├── M314_0.6.txt │ │ ├── M315_0.6.txt │ │ ├── M322_0.6.txt │ │ ├── M324_0.6.txt │ │ ├── M326_0.6.txt │ │ ├── M327_0.6.txt │ │ ├── M335_0.6.txt │ │ ├── M336_0.6.txt │ │ ├── M339_0.6.txt │ │ ├── M340_0.6.txt │ │ ├── M341_0.6.txt │ │ ├── M342_0.6.txt │ │ ├── M355_0.6.txt │ │ ├── M356_0.6.txt │ │ ├── M357_0.6.txt │ │ ├── M286_0.6.txt │ │ ├── M316_0.6.txt │ │ ├── M275_0.6.txt │ │ ├── M297_0.6.txt │ │ ├── M261_0.6.txt │ │ ├── M254_0.6.txt │ │ ├── M307_0.6.txt │ │ ├── M246_0.6.txt │ │ ├── M298_0.6.txt │ │ ├── M344_0.6.txt │ │ ├── M292_0.6.txt │ │ ├── M319_0.6.txt │ │ ├── M291_0.6.txt │ │ ├── M272_0.6.txt │ │ ├── M320_0.6.txt │ │ ├── M269_0.6.txt │ │ ├── M329_0.6.txt │ │ ├── M348_0.6.txt │ │ ├── M262_0.6.txt │ │ ├── M353_0.6.txt │ │ ├── M350_0.6.txt │ │ ├── M250_0.6.txt │ │ ├── M271_0.6.txt │ │ ├── M317_0.6.txt │ │ ├── M318_0.6.txt │ │ ├── M247_0.6.txt │ │ ├── M296_0.6.txt │ │ ├── M346_0.6.txt │ │ ├── M334_0.6.txt │ │ ├── M349_0.6.txt │ │ ├── M330_0.6.txt │ │ ├── M290_0.6.txt │ │ ├── M273_0.6.txt │ │ ├── M333_0.6.txt │ │ ├── M245_0.6.txt │ │ ├── M347_0.6.txt │ │ ├── M274_0.6.txt │ │ ├── M354_0.6.txt │ │ ├── M256_0.6.txt │ │ ├── M345_0.6.txt │ │ ├── M323_0.6.txt │ │ ├── M332_0.6.txt │ │ ├── M013_0.6.txt │ │ ├── M043_0.6.txt │ │ ├── M054_0.6.txt │ │ ├── M159_0.6.txt │ │ ├── M177_0.6.txt │ │ ├── M017_0.6.txt │ │ ├── M140_0.6.txt │ │ ├── M175_0.6.txt │ │ ├── M210_0.6.txt │ │ ├── M016_0.6.txt │ │ ├── M026_0.6.txt │ │ ├── M027_0.6.txt │ │ ├── M032_0.6.txt │ │ ├── M042_0.6.txt │ │ ├── M044_0.6.txt │ │ ├── M048_0.6.txt │ │ ├── M055_0.6.txt │ │ ├── M056_0.6.txt │ │ ├── M072_0.6.txt │ │ ├── M073_0.6.txt │ │ ├── M145_0.6.txt │ │ ├── M155_0.6.txt │ │ ├── M161_0.6.txt │ │ ├── M163_0.6.txt │ │ ├── M167_0.6.txt │ │ ├── M168_0.6.txt │ │ ├── M242_0.6.txt │ │ ├── M243_0.6.txt │ │ ├── M260_0.6.txt │ │ ├── M352_0.6.txt │ │ ├── M004_0.6.txt │ │ ├── M020_0.6.txt │ │ ├── M021_0.6.txt │ │ ├── M023_0.6.txt │ │ ├── M024_0.6.txt │ │ ├── M035_0.6.txt │ │ ├── M036_0.6.txt │ │ ├── M040_0.6.txt │ │ ├── M052_0.6.txt │ │ ├── M053_0.6.txt │ │ ├── M060_0.6.txt │ │ ├── M065_0.6.txt │ │ ├── M068_0.6.txt │ │ ├── M089_0.6.txt │ │ ├── M108_0.6.txt │ │ ├── M112_0.6.txt │ │ ├── M126_0.6.txt │ │ ├── M141_0.6.txt │ │ ├── M143_0.6.txt │ │ ├── M144_0.6.txt │ │ ├── M153_0.6.txt │ │ ├── M156_0.6.txt │ │ ├── M157_0.6.txt │ │ ├── M162_0.6.txt │ │ ├── M164_0.6.txt │ │ ├── M176_0.6.txt │ │ ├── M178_0.6.txt │ │ ├── M201_0.6.txt │ │ ├── M211_0.6.txt │ │ ├── M227_0.6.txt │ │ ├── M228_0.6.txt │ │ ├── M231_0.6.txt │ │ ├── M234_0.6.txt │ │ ├── M236_0.6.txt │ │ ├── M037_0.6.txt │ │ ├── M046_0.6.txt │ │ ├── M047_0.6.txt │ │ ├── M061_0.6.txt │ │ ├── M069_0.6.txt │ │ ├── M075_0.6.txt │ │ ├── M079_0.6.txt │ │ ├── M083_0.6.txt │ │ ├── M101_0.6.txt │ │ ├── M121_0.6.txt │ │ ├── M127_0.6.txt │ │ ├── M138_0.6.txt │ │ ├── M151_0.6.txt │ │ ├── M154_0.6.txt │ │ ├── M169_0.6.txt │ │ ├── M209_0.6.txt │ │ ├── M229_0.6.txt │ │ ├── M235_0.6.txt │ │ ├── M012_0.6.txt │ │ ├── M019_0.6.txt │ │ ├── M049_0.6.txt │ │ ├── M082_0.6.txt │ │ ├── M086_0.6.txt │ │ ├── M087_0.6.txt │ │ ├── M102_0.6.txt │ │ ├── M109_0.6.txt │ │ ├── M120_0.6.txt │ │ ├── M146_0.6.txt │ │ ├── M160_0.6.txt │ │ ├── M232_0.6.txt │ │ ├── M238_0.6.txt │ │ ├── M001_0.6.txt │ │ ├── M002_0.6.txt │ │ ├── M008_0.6.txt │ │ ├── M022_0.6.txt │ │ ├── M025_0.6.txt │ │ ├── M031_0.6.txt │ │ ├── M050_0.6.txt │ │ ├── M051_0.6.txt │ │ ├── M062_0.6.txt │ │ ├── M077_0.6.txt │ │ ├── M078_0.6.txt │ │ ├── M081_0.6.txt │ │ ├── M088_0.6.txt │ │ ├── M097_0.6.txt │ │ ├── M099_0.6.txt │ │ ├── M100_0.6.txt │ │ ├── M103_0.6.txt │ │ ├── M104_0.6.txt │ │ ├── M105_0.6.txt │ │ ├── M111_0.6.txt │ │ ├── M113_0.6.txt │ │ ├── M117_0.6.txt │ │ ├── M124_0.6.txt │ │ ├── M142_0.6.txt │ │ ├── M147_0.6.txt │ │ ├── M148_0.6.txt │ │ ├── M149_0.6.txt │ │ ├── M150_0.6.txt │ │ ├── M158_0.6.txt │ │ ├── M170_0.6.txt │ │ ├── M045_0.6.txt │ │ ├── M098_0.6.txt │ │ ├── M195_0.6.txt │ │ ├── M244_0.6.txt │ │ ├── M351_0.6.txt │ │ ├── M074_0.6.txt │ │ ├── M331_0.6.txt │ │ ├── M033_0.6.txt │ │ ├── M070_0.6.txt │ │ ├── M106_0.6.txt │ │ ├── M122_0.6.txt │ │ ├── M134_0.6.txt │ │ ├── M152_0.6.txt │ │ ├── M188_0.6.txt │ │ ├── M205_0.6.txt │ │ ├── M207_0.6.txt │ │ ├── M233_0.6.txt │ │ ├── M237_0.6.txt │ │ ├── M071_0.6.txt │ │ ├── M085_0.6.txt │ │ ├── M136_0.6.txt │ │ ├── M240_0.6.txt │ │ ├── M118_0.6.txt │ │ ├── M325_0.6.txt │ │ ├── M328_0.6.txt │ │ └── M287_0.6.txt └── Models │ ├── DeepLncRNA │ └── dlgrid_model_483 ├── src ├── LncRNA_subcell.docx ├── lnclocator_parse.R ├── DATA_Acq.md ├── DeepLncRNA.R └── LncRNA_subcell.Rmd ├── .gitignore ├── LICENSE └── README.md /Data/Motifs/pwms_all_motifs/M249_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M255_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M259_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M263_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M264_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M265_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M266_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M267_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M268_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M270_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M280_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M281_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M283_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M284_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M285_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M293_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M294_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M295_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M301_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M302_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M303_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M304_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M305_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M308_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M309_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M310_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M311_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M312_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M313_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M314_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M315_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M322_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M324_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M326_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M327_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M335_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M336_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M339_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M340_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M341_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M342_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M355_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M356_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M357_0.6.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Data/Models/DeepLncRNA: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bgudenas/DeepLncRNA/HEAD/Data/Models/DeepLncRNA -------------------------------------------------------------------------------- /src/LncRNA_subcell.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bgudenas/DeepLncRNA/HEAD/src/LncRNA_subcell.docx -------------------------------------------------------------------------------- /Data/Models/dlgrid_model_483: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bgudenas/DeepLncRNA/HEAD/Data/Models/dlgrid_model_483 -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M286_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 0 0 1 3 | 2 0 0 1 0 4 | 3 0 0 0 1 5 | 4 1 0 0 0 6 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M316_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 0 1 0 3 | 2 0 0 1 0 4 | 3 0 0 0 1 5 | 4 0 0 1 0 6 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | /Data/ 6 | /Figures 7 | /src/DTE_cache 8 | /Manuscript 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M275_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 1 0 0 0 3 | 2 1 0 0 0 4 | 3 1 0 0 0 5 | 4 1 0 0 0 6 | 5 1 0 0 0 7 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M297_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 0 1 0 3 | 2 0 1 0 0 4 | 3 1 0 0 0 5 | 4 0 0.125 0 0.875 6 | 5 0 0 1 0 7 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M261_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 0 0.75 0.25 3 | 2 0 0.25 0 0.75 4 | 3 0 0 1 0 5 | 4 0 0 0 1 6 | 5 0 0 1 0 7 | 6 1 0 0 0 8 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M254_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 1 0 0 0 3 | 2 1 0 0 0 4 | 3 0 0.8 0.1 0.1 5 | 4 1 0 0 0 6 | 5 0.1 0.2 0 0.7 7 | 6 0 0.9 0 0.1 8 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M307_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 1 0 0 0 3 | 2 0 0 1 0 4 | 3 0 0 1 0 5 | 4 0 0 1 0 6 | 5 0.89655172413793 0 0 0.10344827586207 7 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M246_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 1 0 0 3 | 2 0.31578947368421 0.026315789473684 0 0.65789473684211 4 | 3 0 1 0 0 5 | 4 1 0 0 0 6 | 5 1 0 0 0 7 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M298_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.042553191489362 0 0 0.95744680851064 3 | 2 0 0 1 0 4 | 3 0 1 0 0 5 | 4 1 0 0 0 6 | 5 0 0 0 1 7 | 6 0 0 1 0 8 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M344_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 1 0 0 3 | 2 0 1 0 0 4 | 3 0.66666666666667 0.33333333333333 0 0 5 | 4 0 0.25 0.41666666666667 0.33333333333333 6 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M292_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.10526315789474 0 0.89473684210526 0 3 | 2 0 0 1 0 4 | 3 1 0 0 0 5 | 4 0.68421052631579 0.26315789473684 0.052631578947368 0 6 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M319_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 1 0 0 0 3 | 2 0.090909090909091 0 0 0.90909090909091 4 | 3 0 0 0 1 5 | 4 0 0 1 0 6 | 5 0 1 0 0 7 | 6 1 0 0 0 8 | 7 0 1 0 0 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M291_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.16 0.16 0.68 0 3 | 2 0 0.68 0.04 0.28 4 | 3 0.12 0.2 0.44 0.24 5 | 4 0 0 1 0 6 | 5 0.44 0 0.56 0 7 | 6 1 0 0 0 8 | 7 0.36 0.64 0 0 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M272_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.55 0.05 0.3 0.1 3 | 2 0 0.05 0.95 0 4 | 3 0.85 0 0.1 0.05 5 | 4 0.8 0.05 0.1 0.05 6 | 5 0.05 0.05 0.85 0.05 7 | 6 0.6 0 0.4 0 8 | 7 0.75 0 0.25 0 9 | 8 0 0.9 0 0.1 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M320_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 0.42009132420091 0 0.57990867579909 3 | 2 0 0.0045662100456621 0.99543378995434 0 4 | 3 0 0.99543378995434 0.0045662100456621 0 5 | 4 0 0.19634703196347 0 0.80365296803653 6 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M269_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 1 0 0 0 3 | 2 1 0 0 0 4 | 3 0.4 0.2 0 0.4 5 | 4 1 0 0 0 6 | 5 1 0 0 0 7 | 6 0.6 0 0.4 0 8 | 7 0 0.2 0.4 0.4 9 | 8 1 0 0 0 10 | 9 1 0 0 0 11 | 10 1 0 0 0 12 | 11 0 0 1 0 13 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M329_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.25 0 0 0.75 3 | 2 0 0.05 0 0.95 4 | 3 0 0 0 1 5 | 4 0 0.05 0.05 0.9 6 | 5 0.9 0 0.1 0 7 | 6 0 0 0.05 0.95 8 | 7 0.2 0 0 0.8 9 | 8 0 0.05 0.1 0.85 10 | 9 0.35 0 0.05 0.6 11 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M348_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.6875 0 0.0625 0.25 3 | 2 0 0.25 0.75 0 4 | 3 0 0 0.9375 0.0625 5 | 4 0.75 0.125 0.125 0 6 | 5 0.0625 0 0.8125 0.125 7 | 6 0.875 0.0625 0.0625 0 8 | 7 0.0625 0.0625 0.125 0.75 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M262_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.070175438596491 0.035087719298246 0.10526315789474 0.78947368421053 3 | 2 1 0 0 0 4 | 3 0 1 0 0 5 | 4 0 0 0 1 6 | 5 1 0 0 0 7 | 6 1 0 0 0 8 | 7 0 0.87719298245614 0 0.12280701754386 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M353_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.72 0.16 0 0.12 3 | 2 0.08 0.88 0 0.04 4 | 3 0 0 0.96 0.04 5 | 4 1 0 0 0 6 | 5 0.04 0 0.72 0.24 7 | 6 0.8 0 0 0.2 8 | 7 0 0.04 0.84 0.12 9 | 8 0.84 0.12 0 0.04 10 | 9 0.24 0.44 0 0.32 11 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M350_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.1875 0.0625 0 0.75 3 | 2 0.0625 0 0.0625 0.875 4 | 3 0.9375 0 0.0625 0 5 | 4 0 0 0 1 6 | 5 0 0 0 1 7 | 6 0 0 0 1 8 | 7 0.875 0.0625 0.0625 0 9 | 8 0.375 0 0 0.625 10 | 9 0.0625 0.125 0.25 0.5625 11 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M250_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 1 0 0 0 3 | 2 1 0 0 0 4 | 3 0 0.76923076923077 0.23076923076923 0 5 | 4 0.92307692307692 0 0 0.076923076923077 6 | 5 0.15384615384615 0.076923076923077 0 0.76923076923077 7 | 6 0 0.84615384615385 0 0.15384615384615 8 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M271_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 0.042553191489362 0 0.95744680851064 3 | 2 1 0 0 0 4 | 3 0 0 1 0 5 | 4 0.021276595744681 0 0.97872340425532 0 6 | 5 0.1063829787234 0.021276595744681 0.78723404255319 0.085106382978723 7 | 6 0.5531914893617 0 0 0.4468085106383 8 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M317_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.77777777777778 0 0 0.22222222222222 3 | 2 0 0 0 1 4 | 3 0.11111111111111 0 0 0.88888888888889 5 | 4 0 0 1 0 6 | 5 0 1 0 0 7 | 6 1 0 0 0 8 | 7 0 1 0 0 9 | 8 0.22222222222222 0.22222222222222 0.11111111111111 0.44444444444444 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M318_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.81818181818182 0.090909090909091 0 0.090909090909091 3 | 2 0.090909090909091 0 0 0.90909090909091 4 | 3 0.090909090909091 0 0 0.90909090909091 5 | 4 0 0 0.90909090909091 0.090909090909091 6 | 5 0 1 0 0 7 | 6 1 0 0 0 8 | 7 0 1 0 0 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M247_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.019230769230769 0.98076923076923 0 0 3 | 2 0.21153846153846 0 0 0.78846153846154 4 | 3 0.019230769230769 0.96153846153846 0 0.019230769230769 5 | 4 0.88461538461538 0.096153846153846 0 0.019230769230769 6 | 5 0.96078431372549 0 0.019607843137255 0.019607843137255 7 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M296_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.91666666666667 0 0.083333333333333 0 3 | 2 0.91666666666667 0 0 0.083333333333333 4 | 3 0 0 1 0 5 | 4 0 1 0 0 6 | 5 1 0 0 0 7 | 6 0 0.75 0 0.25 8 | 7 0 0.75 0.25 0 9 | 8 0 1 0 0 10 | 9 0 0.25 0.75 0 11 | 10 0 0.090909090909091 0 0.90909090909091 12 | 11 0 0 0 1 13 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M346_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.125 0.0625 0.75 0.0625 3 | 2 0.0625 0.0625 0.8125 0.0625 4 | 3 0.0625 0 0.75 0.1875 5 | 4 0.1875 0 0.25 0.5625 6 | 5 0.9375 0 0.0625 0 7 | 6 0.13333333333333 0 0 0.86666666666667 8 | 7 0 0 1 0 9 | 8 0 1 0 0 10 | 9 0 0.125 0.0625 0.8125 11 | 10 0 0 0.9375 0.0625 12 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M334_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 0 1 0 3 | 2 0.75 0 0.25 0 4 | 3 0 0 0 1 5 | 4 0 1 0 0 6 | 5 1 0 0 0 7 | 6 1 0 0 0 8 | 7 0 1 0 0 9 | 8 0 1 0 0 10 | 9 0.5 0.25 0 0.25 11 | 10 0 0 1 0 12 | 11 0 0 1 0 13 | 12 0 1 0 0 14 | 13 0 0 1 0 15 | 14 1 0 0 0 16 | 15 0 1 0 0 17 | 16 0.75 0.25 0 0 18 | 17 0 0 1 0 19 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M349_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 1 0 0 0 3 | 2 0.14285714285714 0.85714285714286 0 0 4 | 3 0.28571428571429 0 0.28571428571429 0.42857142857143 5 | 4 0.85714285714286 0 0.14285714285714 0 6 | 5 1 0 0 0 7 | 6 0 0.28571428571429 0.14285714285714 0.57142857142857 8 | 7 0.42857142857143 0.42857142857143 0.14285714285714 0 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M330_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.33333333333333 0 0 0.66666666666667 3 | 2 0 0 0 1 4 | 3 0 0.16666666666667 0 0.83333333333333 5 | 4 0 0.33333333333333 0 0.66666666666667 6 | 5 0.83333333333333 0 0.16666666666667 0 7 | 6 0.16666666666667 0.16666666666667 0 0.66666666666667 8 | 7 0 0 0 1 9 | 8 0 0 0 1 10 | 9 0 0 0 1 11 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M290_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.076923076923077 0.15384615384615 0.53846153846154 0.23076923076923 3 | 2 0 0.23076923076923 0 0.76923076923077 4 | 3 0.23076923076923 0.30769230769231 0 0.46153846153846 5 | 4 0 0 1 0 6 | 5 0 0 1 0 7 | 6 0.92307692307692 0.076923076923077 0 0 8 | 7 0.69230769230769 0.23076923076923 0 0.076923076923077 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M273_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.82352941176471 0.058823529411765 0.058823529411765 0.058823529411765 3 | 2 0 1 0 0 4 | 3 0 0 1 0 5 | 4 0 0.94117647058824 0.058823529411765 0 6 | 5 0 0 0.88235294117647 0.11764705882353 7 | 6 0.11764705882353 0.88235294117647 0 0 8 | 7 0.52941176470588 0.058823529411765 0.29411764705882 0.11764705882353 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M333_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.81081081081081 0.081081081081081 0 0.10810810810811 3 | 2 0.027027027027027 0.054054054054054 0.91891891891892 0 4 | 3 0.027027027027027 0.27027027027027 0.7027027027027 0 5 | 4 0.89189189189189 0.081081081081081 0 0.027027027027027 6 | 5 0.13513513513514 0.45945945945946 0.32432432432432 0.081081081081081 7 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M245_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.1 0.9 0 0 3 | 2 0.1 0.8 0.05 0.05 4 | 3 0 0.1 0.9 0 5 | 4 0.95 0.05 0 0 6 | 5 1 0 0 0 7 | 6 1 0 0 0 8 | 7 0.1 0 0.45 0.45 9 | 8 0 1 0 0 10 | 9 0 1 0 0 11 | 10 0 1 0 0 12 | 11 0 0 1 0 13 | 12 1 0 0 0 14 | 13 1 0 0 0 15 | 14 0 0.05 0.95 0 16 | 15 0 0 0.05 0.95 17 | 16 1 0 0 0 18 | 17 0.05 0.2 0.65 0.1 19 | 18 0 0.05 0.85 0.1 20 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M347_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.23076923076923 0 0.69230769230769 0.076923076923077 3 | 2 0.46153846153846 0.23076923076923 0.23076923076923 0.076923076923077 4 | 3 0 0 1 0 5 | 4 0 1 0 0 6 | 5 1 0 0 0 7 | 6 0 0 1 0 8 | 7 0 0 0 1 9 | 8 0.92307692307692 0 0.076923076923077 0 10 | 9 0 0 1 0 11 | 10 0 0 0.53846153846154 0.46153846153846 12 | 11 0 0.38461538461538 0.61538461538462 0 13 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M274_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 0 1 0 3 | 2 0.090909090909091 0.090909090909091 0 0.81818181818182 4 | 3 0.090909090909091 0 0 0.90909090909091 5 | 4 0 0.90909090909091 0.090909090909091 0 6 | 5 0 0.27272727272727 0.72727272727273 0 7 | 6 1 0 0 0 8 | 7 0 0 1 0 9 | 8 0.090909090909091 0 0.27272727272727 0.63636363636364 10 | 9 0.54545454545455 0 0.090909090909091 0.36363636363636 11 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M354_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 0.13888888888889 0.47222222222222 0.38888888888889 3 | 2 0.47222222222222 0.36111111111111 0.13888888888889 0.027777777777778 4 | 3 0.41666666666667 0.19444444444444 0.27777777777778 0.11111111111111 5 | 4 0 0 0.055555555555556 0.94444444444444 6 | 5 0.38888888888889 0.22222222222222 0.38888888888889 0 7 | 6 0.055555555555556 0.86111111111111 0.083333333333333 0 8 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M256_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.054545454545455 0.63636363636364 0.14545454545455 0.16363636363636 3 | 2 0.8 0.054545454545455 0.018181818181818 0.12727272727273 4 | 3 0.16363636363636 0 0.81818181818182 0.018181818181818 5 | 4 0.16363636363636 0.072727272727273 0.18181818181818 0.58181818181818 6 | 5 0.2 0.12727272727273 0.63636363636364 0.036363636363636 7 | 6 0.29090909090909 0.4 0.090909090909091 0.21818181818182 8 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M345_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 0 1 0 3 | 2 0.53333333333333 0 0.13333333333333 0.33333333333333 4 | 3 0.2 0 0 0.8 5 | 4 0.33333333333333 0 0 0.66666666666667 6 | 5 0 1 0 0 7 | 6 0 0.86666666666667 0.13333333333333 0 8 | 7 0.33333333333333 0.066666666666667 0 0.6 9 | 8 0 0 1 0 10 | 9 0 0.73333333333333 0 0.26666666666667 11 | 10 0.13333333333333 0.066666666666667 0 0.8 12 | 11 0.93333333333333 0.066666666666667 0 0 13 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M323_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.16666666666667 0 0.83333333333333 0 3 | 2 0.16666666666667 0.25 0.58333333333333 0 4 | 3 0.58333333333333 0 0.41666666666667 0 5 | 4 0 0 1 0 6 | 5 1 0 0 0 7 | 6 0 0 1 0 8 | 7 0.083333333333333 0 0.083333333333333 0.83333333333333 9 | 8 0 1 0 0 10 | 9 1 0 0 0 11 | 10 0 0 0 1 12 | 11 0.33333333333333 0.33333333333333 0 0.33333333333333 13 | 12 0.083333333333333 0.5 0.41666666666667 0 14 | 13 0 0.83333333333333 0 0.16666666666667 15 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M332_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.068965517241379 0 0.20689655172414 0.72413793103448 3 | 2 0 0 1 0 4 | 3 0.068965517241379 0 0 0.93103448275862 5 | 4 0.03448275862069 0 0 0.96551724137931 6 | 5 0 1 0 0 7 | 6 0 0.55172413793103 0.44827586206897 0 8 | 7 0.93103448275862 0 0.03448275862069 0.03448275862069 9 | 8 0 0 1 0 10 | 9 0.58620689655172 0.10344827586207 0.03448275862069 0.27586206896552 11 | 10 0.17241379310345 0.03448275862069 0.13793103448276 0.6551724137931 12 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M013_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.012021481040213 0.012021481040213 0.012021481040213 0.963935552230588 3 | 2 0.963935552230588 0.012021481040213 0.012021481040213 0.012021481040213 4 | 3 0.10164370706502 0.012021481040213 0.87431332620578 0.012021481040213 5 | 4 0.11753403355671 0.012021481040213 0.670501924945205 0.199942555809099 6 | 5 0.201960375046139 0.012021481040213 0.0992223239805725 0.686795815284302 7 | 6 0.686795815284302 0.012021481040213 0.0979107414764966 0.203271957550215 8 | 7 0.337267846220653 0.0591582052159025 0.544415746060043 0.0591582052159025 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M043_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.046319513823871 0.779292093387599 0.046319513823871 0.128068869766166 3 | 2 0.024144469689902 0.763613049142094 0.024144469689902 0.188098000096267 4 | 3 0.024144469689902 0.311333882444892 0.024144469689902 0.640377166793469 5 | 4 0.105624137096151 0.311333882444892 0.024144469689902 0.558897499387218 6 | 5 0.108038612109826 0.734923404861957 0.024144469689902 0.132893501956478 7 | 6 0.024144469689902 0.927566579548458 0.024144469689902 0.024144469689902 8 | 7 0.157967068788357 0.625488077050551 0.0680608582803663 0.148483991353379 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M054_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.194887459259023 0.11287264514794 0.579367260795829 0.11287264514794 3 | 2 0.020971104313817 0.669653480854894 0.020971104313817 0.28840431700041 4 | 3 0.020971104313817 0.0989011690249422 0.859156628830363 0.020971104313817 5 | 4 0.020971104313817 0.859156628830363 0.0989011690249422 0.020971104313817 6 | 5 0.020971104313817 0.0989011690249422 0.859156628830363 0.020971104313817 7 | 6 0.020971104313817 0.846311112655497 0.111746685199807 0.020971104313817 8 | 7 0.0666382930280382 0.157225475551184 0.61443434023537 0.161701901527663 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M159_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.312096560381765 0.0517475986102623 0.0517475986102623 0.584408242979162 3 | 2 0.004218445786123 0.004218445786123 0.98734466264412 0.004218445786123 4 | 3 0.004218445786123 0.98734466264412 0.004218445786123 0.004218445786123 5 | 4 0.98734466264412 0.004218445786123 0.004218445786123 0.004218445786123 6 | 5 0.004218445786123 0.004218445786123 0.004218445786123 0.98734466264412 7 | 6 0.004218445786123 0.004218445786123 0.98734466264412 0.004218445786123 8 | 7 0.313687816216559 0.481444869244603 0.102433657159761 0.102433657159761 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M177_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0607771303349761 0.817668603528926 0.0607771303349761 0.0607771303349761 3 | 2 0.102003277503341 0.868662521229795 0.014667100382603 0.014667100382603 4 | 3 0.291028483512214 0.110004579925396 0.014667100382603 0.584299835678128 5 | 4 0.373745352018156 0.014667100382603 0.014667100382603 0.596920446714979 6 | 5 0.38479869763213 0.19156662127764 0.014667100382603 0.408967580205969 7 | 6 0.014667100382603 0.955998698350532 0.014667100382603 0.014667100382603 8 | 7 0.014667100382603 0.955998698350532 0.014667100382603 0.014667100382603 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M017_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.298745043927636 0.0512258035946438 0.0512258035946438 0.598803348190284 3 | 2 0.003967692980552 0.003967692980552 0.988096922085338 0.003967692980552 4 | 3 0.003967692980552 0.988096922085338 0.003967692980552 0.003967692980552 5 | 4 0.988096922085338 0.003967692980552 0.003967692980552 0.003967692980552 6 | 5 0.003967692980552 0.003967692980552 0.003967692980552 0.988096922085338 7 | 6 0.003967692980552 0.003967692980552 0.988096922085338 0.003967692980552 8 | 7 0.405194573634082 0.389106701227325 0.102849361903183 0.102849361903183 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M140_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.343505630007997 0.43793822555621 0.066672841334629 0.151883307423822 3 | 2 0.584888576436 0.145253214253333 0.226538599737026 0.0433196042887447 4 | 3 0.0195968961573603 0.11992478349319 0.660548608914677 0.199929710226291 5 | 4 0.941209310319437 0.0195968961573603 0.0195968961573603 0.0195968961573603 6 | 5 0.0195968961573603 0.853150122702307 0.0195968961573603 0.107656083774492 7 | 6 0.84912299226029 0.0195968961573603 0.111683214216507 0.0195968961573603 8 | 7 0.0653433824274698 0.0653433824274698 0.803969854520466 0.0653433824274698 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M175_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.47180393842836 0.0812586920384489 0.0812586920384489 0.365678677404633 3 | 2 0.009062811327394 0.009062811327394 0.972811566173626 0.009062811327394 4 | 3 0.292600891493123 0.009062811327394 0.009062811327394 0.689273486007894 5 | 4 0.009062811327394 0.009062811327394 0.972811566173626 0.009062811327394 6 | 5 0.009062811327394 0.009062811327394 0.009062811327394 0.972811566173626 7 | 6 0.009062811327394 0.009062811327394 0.972811566173626 0.009062811327394 8 | 7 0.535514698500703 0.0573267983817584 0.157537103319216 0.249621402755809 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M210_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.265392701879802 0.0857816565481827 0.0857816565481827 0.56304398409449 3 | 2 0.645599216469742 0.0597210794347362 0.234958625372078 0.0597210794347362 4 | 3 0.011707427774039 0.011707427774039 0.877865413308838 0.0987197272945287 5 | 4 0.686838334144168 0.011707427774039 0.10897247912791 0.192481755105328 6 | 5 0.101069316256345 0.011707427774039 0.011707427774039 0.875515824347022 7 | 6 0.875515824347022 0.011707427774039 0.011707427774039 0.101069316256345 8 | 7 0.123901364191983 0.0352529546076604 0.805592721263838 0.0352529546076604 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M016_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.110871349592076 0.110871349592076 0.576230667329126 0.20202663331605 3 | 2 0.0183331335327331 0.0183331335327331 0.94500060058715 0.0183331335327331 4 | 3 0.94500060058715 0.0183331335327331 0.0183331335327331 0.0183331335327331 5 | 4 0.0183331335327331 0.94500060058715 0.0183331335327331 0.0183331335327331 6 | 5 0.766209687874068 0.0183331335327331 0.197124046245815 0.0183331335327331 7 | 6 0.499700431433382 0.0414525935076519 0.417394376983791 0.0414525935076519 8 | 7 0.133741033785827 0.0414525935076519 0.783353774631347 0.0414525935076519 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M026_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.109804549527276 0.856031637939824 0.0170819044177939 0.0170819044177939 3 | 2 0.108255211143277 0.76485833121434 0.0170819044177939 0.109804549527276 4 | 3 0.856031637939824 0.0170819044177939 0.0170819044177939 0.109804549527276 5 | 4 0.593491811528232 0.0170819044177939 0.103135658222238 0.286290622134421 6 | 5 0.312760833839568 0.502420296283448 0.040993376028484 0.143825489481627 7 | 6 0.0642751501391216 0.807174542424277 0.0642751501391216 0.0642751501391216 8 | 7 0.0880498710944913 0.735850379141296 0.0880498710944913 0.0880498710944913 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M027_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.737562985257612 0.146785196267679 0.0578259110965854 0.0578259110965854 3 | 2 0.191432559536191 0.686074285555823 0.0111137710069721 0.111379381229144 4 | 3 0.966658684307214 0.0111137710069721 0.0111137710069721 0.0111137710069721 5 | 4 0.11028326236173 0.67147398224186 0.0111137710069721 0.207128981717569 6 | 5 0.88412827735981 0.0111137710069721 0.0111137710069721 0.0936441779543756 7 | 6 0.274028733615639 0.703743721698546 0.0111137710069721 0.0111137710069721 8 | 7 0.716364903447614 0.213975591094505 0.034829755217311 0.034829755217311 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M032_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.564544750782044 0.176611111265786 0.171979417647919 0.0868647226646405 3 | 2 0.399782829826952 0.5206986972781 0.0397592373599863 0.0397592373599863 4 | 3 0.951032580838079 0.0163224706475051 0.0163224706475051 0.0163224706475051 5 | 4 0.507026175490207 0.199209200887384 0.0163224706475051 0.277442145755497 6 | 5 0.596933445232028 0.109301931145564 0.0163224706475051 0.277442145755497 7 | 6 0.109301931145564 0.85805312034002 0.0163224706475051 0.0163224706475051 8 | 7 0.951032580838079 0.0163224706475051 0.0163224706475051 0.0163224706475051 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M042_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.7784371010493 0.10307987171858 0.110525483304575 0.0079575404738413 3 | 2 0.790962791373655 0.103881309076795 0.0971983556220047 0.0079575404738413 4 | 3 0.976127375124768 0.0079575404738413 0.0079575404738413 0.0079575404738413 5 | 4 0.976127375124768 0.0079575404738413 0.0079575404738413 0.0079575404738413 6 | 5 0.976127375124768 0.0079575404738413 0.0079575404738413 0.0079575404738413 7 | 6 0.684736674794941 0.111016686846707 0.103752044986761 0.100494589917888 8 | 7 0.682707228581397 0.104799084116041 0.204536143375017 0.0079575404738413 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M044_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0869664872741963 0.360842894195759 0.465224124250878 0.0869664872741963 3 | 2 0.0185059653053864 0.572626211949122 0.297104793735792 0.111763023698642 4 | 3 0.0185059653053864 0.20589934215392 0.75708872192425 0.0185059653053864 5 | 4 0.0185059653053864 0.944482098772784 0.0185059653053864 0.0185059653053864 6 | 5 0.0185059653053864 0.109711416887259 0.853276647190911 0.0185059653053864 7 | 6 0.0185059653053864 0.856793687438998 0.106194376639172 0.0185059653053864 8 | 7 0.064957077214725 0.340097816109821 0.52998803647158 0.064957077214725 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M048_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.169305997055016 0.0824047674715971 0.665884473058981 0.0824047674715971 3 | 2 0.719593993508974 0.0367687437588604 0.20686852549348 0.0367687437588604 4 | 3 0.184494469046595 0.0133316901580824 0.191715079000144 0.610458758785568 5 | 4 0.960004926516143 0.0133316901580824 0.0133316901580824 0.0133316901580824 6 | 5 0.191715079000144 0.781621537674081 0.0133316901580824 0.0133316901580824 7 | 6 0.125075037120515 0.0365470770429918 0.597009060218934 0.24136882568045 8 | 7 0.682840496763612 0.105719834126826 0.105719834126826 0.105719834126826 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M055_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.582687365632857 0.202666001401069 0.107323318360732 0.107323318360732 3 | 2 0.0117134313700685 0.108039792523197 0.0117134313700685 0.868533344794977 4 | 3 0.964859705948105 0.0117134313700685 0.0117134313700685 0.0117134313700685 5 | 4 0.0117134313700685 0.0117134313700685 0.0117134313700685 0.964859705948105 6 | 5 0.964859705948105 0.0117134313700685 0.0117134313700685 0.0117134313700685 7 | 6 0.1043516992496 0.105547837608604 0.217822710215122 0.572277752984984 8 | 7 0.52478391012339 0.356883889079257 0.0591660992812212 0.0591660992812212 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M056_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.69288052651345 0.0343792333552597 0.0343792333552597 0.238361007705729 3 | 2 0.0106054833785244 0.9681835524885 0.0106054833785244 0.0106054833785244 4 | 3 0.9681835524885 0.0106054833785244 0.0106054833785244 0.0106054833785244 5 | 4 0.9681835524885 0.0106054833785244 0.0106054833785244 0.0106054833785244 6 | 5 0.0106054833785244 0.9681835524885 0.0106054833785244 0.0106054833785244 7 | 6 0.326700440535904 0.0342729169418406 0.604753730778475 0.0342729169418406 8 | 7 0.483254128968136 0.107242309936264 0.302261249915419 0.107242309936264 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M072_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.884672315346734 0.0384425633893717 0.0384425633893717 0.0384425633893717 3 | 2 0.10058950956679 0.0150743579638745 0.68209638168666 0.202239755216509 4 | 3 0.101696819942551 0.0150743579638745 0.868154468563533 0.0150743579638745 5 | 4 0.782639316960617 0.0150743579638745 0.10058950956679 0.101696819942551 6 | 5 0.195200424970599 0.207539026300508 0.49643376280113 0.100826790361596 7 | 6 0.294161488279185 0.675689800226899 0.0150743579638745 0.0150743579638745 8 | 7 0.645465947259644 0.0861537456618248 0.182226566276379 0.0861537456618248 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M073_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.199424614721753 0.575804567268075 0.112385411830917 0.112385411830917 3 | 2 0.213060514297798 0.112385411830917 0.56216866769203 0.112385411830917 4 | 3 0.866619154617786 0.0444602789390008 0.0444602789390008 0.0444602789390008 5 | 4 0.0217296766083052 0.0217296766083052 0.0217296766083052 0.934810973285192 6 | 5 0.934810973285192 0.0217296766083052 0.0217296766083052 0.0217296766083052 7 | 6 0.0676404753354623 0.707759806226912 0.0676404753354623 0.156959250407058 8 | 7 0.0903433244793605 0.0903433244793605 0.0903433244793605 0.7289700254379 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M145_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0634475298679768 0.270051416875072 0.603053516487808 0.0634475298679768 3 | 2 0.878566052954076 0.0404779808168179 0.0404779808168179 0.0404779808168179 4 | 3 0.668123496966648 0.106939882795166 0.118834373937212 0.106102242573895 5 | 4 0.0173461894732255 0.196701104161361 0.768606513165109 0.0173461894732255 6 | 5 0.0173461894732255 0.10710741083942 0.85820020648705 0.0173461894732255 7 | 6 0.700285216186242 0.0404577148205863 0.218799362515376 0.0404577148205863 8 | 7 0.151742262229696 0.0632265887291975 0.721804557557504 0.0632265887291975 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M155_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0907682404906852 0.180151857140958 0.1781816578809 0.550898248191849 3 | 2 0.0199239224943476 0.0199239224943476 0.854568986608572 0.105583168147867 4 | 3 0.0199239224943476 0.0199239224943476 0.0199239224943476 0.94022823226209 5 | 4 0.0199239224943476 0.0199239224943476 0.129432524972886 0.830719629783553 6 | 5 0.0199239224943476 0.572492640798828 0.38765951395761 0.0199239224943476 7 | 6 0.0199239224943476 0.0199239224943476 0.656334792599012 0.303817362157426 8 | 7 0.066065187365222 0.066065187365222 0.152229535786847 0.715640095358957 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M161_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.457687607024785 0.278486995143315 0.0863405493602015 0.177484853839664 3 | 2 0.860464297674414 0.0159858130385311 0.0159858130385311 0.107564075508787 4 | 3 0.0159858130385311 0.0159858130385311 0.0159858130385311 0.95204256014467 5 | 4 0.0159858130385311 0.95204256014467 0.0159858130385311 0.0159858130385311 6 | 5 0.0159858130385311 0.95204256014467 0.0159858130385311 0.0159858130385311 7 | 6 0.95204256014467 0.0159858130385311 0.0159858130385311 0.0159858130385311 8 | 7 0.278215475391954 0.086146150080073 0.54949222127343 0.086146150080073 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M163_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.71339123964659 0.161112421195536 0.0627481663279934 0.0627481663279934 3 | 2 0.396294530223585 0.487741564026364 0.0155883576168768 0.10037555329662 4 | 3 0.784814912894653 0.0992211813552945 0.0155883576168768 0.10037555329662 5 | 4 0.38750354390118 0.298010062614492 0.0155883576168768 0.298898041030897 6 | 5 0.575991875530085 0.109521730985588 0.0155883576168768 0.298898041030897 7 | 6 0.199370403638837 0.769452886290855 0.0155883576168768 0.0155883576168768 8 | 7 0.863386259659566 0.105437030270127 0.0155883576168768 0.0155883576168768 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M167_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0345599217136254 0.0345599217136254 0.0345599217136254 0.896320230826985 3 | 2 0.966920599644187 0.0110264664414731 0.0110264664414731 0.0110264664414731 4 | 3 0.0110264664414731 0.0110264664414731 0.966920599644187 0.0110264664414731 5 | 4 0.110708273625208 0.100671958864918 0.202113005130197 0.586506761348283 6 | 5 0.361518820358638 0.0110264664414731 0.100974778706823 0.526479933461672 7 | 6 0.56358453575312 0.0577262188138635 0.320963025342606 0.0577262188138635 8 | 7 0.102479925693738 0.102479925693738 0.69256022136361 0.102479925693738 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M168_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.088446272006591 0.088446272006591 0.64373128728228 0.179376168620637 3 | 2 0.0426864246498578 0.0426864246498578 0.134522257838897 0.780104887898506 4 | 3 0.483217102884452 0.0191687652790634 0.390884609854576 0.106729513396931 5 | 4 0.193813087023597 0.0191687652790634 0.680606742042899 0.106411397069464 6 | 5 0.121680980787894 0.0191687652790634 0.106729513396931 0.752420731951134 7 | 6 0.0419317486496899 0.0419317486496899 0.591886975063281 0.324249525895581 8 | 7 0.0872249858436252 0.0872249858436252 0.26202317651027 0.563526860920609 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M242_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.193258417289595 0.591724632504151 0.107508474550001 0.107508474550001 3 | 2 0.304322580751826 0.620185709681961 0.03774585205601 0.03774585205601 4 | 3 0.956594301003039 0.0144685657459802 0.0144685657459802 0.0144685657459802 5 | 4 0.956594301003039 0.0144685657459802 0.0144685657459802 0.0144685657459802 6 | 5 0.956594301003039 0.0144685657459802 0.0144685657459802 0.0144685657459802 7 | 6 0.220723709423621 0.0379189994430454 0.124370105802725 0.616987183406632 8 | 7 0.061555977457034 0.234873378801513 0.061555977457034 0.642014672966831 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M243_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.5411998221913 0.339947632978118 0.0594262717616106 0.0594262717616106 3 | 2 0.896559123705535 0.0344802905566124 0.0344802905566124 0.0344802905566124 4 | 3 0.967547573685047 0.0108174748430969 0.0108174748430969 0.0108174748430969 5 | 4 0.87361964218399 0.0108174748430969 0.0108174748430969 0.104745406344153 6 | 5 0.87361964218399 0.0108174748430969 0.0108174748430969 0.104745406344153 7 | 6 0.778517138694284 0.11179283827606 0.0108174748430969 0.0988725464008965 8 | 7 0.0578837657317887 0.143664793178056 0.653668899979576 0.144782543141504 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M260_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.11111111111111 0 0.77777777777778 0.11111111111111 3 | 2 0.055555555555556 0.77777777777778 0.11111111111111 0.055555555555556 4 | 3 0.055555555555556 0.94444444444444 0 0 5 | 4 0.72222222222222 0.11111111111111 0 0.16666666666667 6 | 5 0.11111111111111 0.44444444444444 0.22222222222222 0.22222222222222 7 | 6 0.88888888888889 0 0 0.11111111111111 8 | 7 0.33333333333333 0.66666666666667 0 0 9 | 8 0 1 0 0 10 | 9 1 0 0 0 11 | 10 0 0.5 0 0.5 12 | 11 0 1 0 0 13 | 12 0 0 1 0 14 | 13 0.055555555555556 0.83333333333333 0 0.11111111111111 15 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M352_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.88461538461538 0.038461538461538 0.038461538461538 0.038461538461538 3 | 2 0.038461538461538 0.038461538461538 0.92307692307692 0 4 | 3 0.038461538461538 0.46153846153846 0.5 0 5 | 4 0.80769230769231 0.15384615384615 0.038461538461538 0 6 | 5 0 0 1 0 7 | 6 0.73076923076923 0.076923076923077 0.038461538461538 0.15384615384615 8 | 7 0.11538461538462 0 0.84615384615385 0.038461538461538 9 | 8 0.23076923076923 0.038461538461538 0.19230769230769 0.53846153846154 10 | 9 0.46153846153846 0.076923076923077 0.11538461538462 0.34615384615385 11 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M004_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0850634504936057 0.0850634504936057 0.175951658141761 0.65392143623043 3 | 2 0.0130464984118041 0.0130464984118041 0.776576805287808 0.197330201099004 4 | 3 0.0130464984118041 0.0130464984118041 0.0130464984118041 0.960860507975009 5 | 4 0.0130464984118041 0.0130464984118041 0.764576198088384 0.20933080829843 6 | 5 0.0130464984118041 0.0130464984118041 0.104633577159811 0.869273429227003 7 | 6 0.0130464984118041 0.0130464984118041 0.666799025115857 0.307107981270957 8 | 7 0.0831008331277267 0.0831008331277267 0.264547858016938 0.56925047512411 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M020_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.178193502140083 0.0872748171298672 0.559955658611622 0.174576018853948 3 | 2 0.0187091904613737 0.0187091904613737 0.943872429890684 0.0187091904613737 4 | 3 0.943872429890684 0.0187091904613737 0.0187091904613737 0.0187091904613737 5 | 4 0.0187091904613737 0.943872429890684 0.0187091904613737 0.0187091904613737 6 | 5 0.390029702673727 0.0187091904613737 0.572551917678331 0.0187091904613737 7 | 6 0.467654595207375 0.0187091904613737 0.494927025144681 0.0187091904613737 8 | 7 0.236166926814529 0.0418072619199785 0.680218543574584 0.0418072619199785 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M021_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.742366063976806 0.0581777369833999 0.0581777369833999 0.141278459156637 3 | 2 0.0345082646186025 0.0345082646186025 0.896475201416213 0.0345082646186025 4 | 3 0.0109308534433254 0.0109308534433254 0.967207439104606 0.0109308534433254 5 | 4 0.967207439104606 0.0109308534433254 0.0109308534433254 0.0109308534433254 6 | 5 0.0109308534433254 0.0109308534433254 0.0109308534433254 0.967207439104606 7 | 6 0.310913414147557 0.0109308534433254 0.480632010561457 0.197523721282244 8 | 7 0.608185248518451 0.0109308534433254 0.28109542448086 0.0997884729919465 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M023_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.177970192173746 0.0861306541812456 0.26726181043746 0.468637347084201 3 | 2 0.0130996148949014 0.0130996148949014 0.0130996148949014 0.960701149831704 4 | 3 0.960701149831704 0.0130996148949014 0.0130996148949014 0.0130996148949014 5 | 4 0.0130996148949014 0.0130996148949014 0.960701149831704 0.0130996148949014 6 | 5 0.0130996148949014 0.0130996148949014 0.960701149831704 0.0130996148949014 7 | 6 0.0364714854774028 0.0364714854774028 0.799054936957703 0.128002090532653 8 | 7 0.452983499712739 0.0827790329891177 0.0827790329891177 0.381458429585513 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M024_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.293787072460145 0.10669127911739 0.294856998578936 0.304664654667863 3 | 2 0.0582383292763632 0.0582383292763632 0.0582383292763632 0.825285010553876 4 | 3 0.967610692986855 0.0107964367267484 0.0107964367267484 0.0107964367267484 5 | 4 0.0107964367267484 0.0107964367267484 0.967610692986855 0.0107964367267484 6 | 5 0.0107964367267484 0.0107964367267484 0.967610692986855 0.0107964367267484 7 | 6 0.0107964367267484 0.0107964367267484 0.967610692986855 0.0107964367267484 8 | 7 0.65932135338852 0.0823856706911844 0.0823856706911844 0.175907308208913 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M035_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.304005719239733 0.38739797531058 0.109358457066392 0.1992378419614 3 | 2 0.0392662279417396 0.0392662279417396 0.882201309138528 0.0392662279417396 4 | 3 0.0392662279417396 0.0392662279417396 0.882201309138528 0.0392662279417396 5 | 4 0.882201309138528 0.0392662279417396 0.0392662279417396 0.0392662279417396 6 | 5 0.0155160569156276 0.0155160569156276 0.953451834693837 0.0155160569156276 7 | 6 0.695453720462072 0.0392662279417396 0.0392662279417396 0.226013816618194 8 | 7 0.719902251897349 0.0625531467635553 0.15499146140642 0.0625531467635553 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M036_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.458380704689553 0.367197490310543 0.0872109044563551 0.0872109044563551 3 | 2 0.865132892167346 0.0171923089037042 0.0171923089037042 0.100482487992784 4 | 3 0.100653792821114 0.0171923089037042 0.0171923089037042 0.864961587339017 5 | 4 0.0171923089037042 0.948423071256426 0.0171923089037042 0.0171923089037042 6 | 5 0.0171923089037042 0.0171923089037042 0.0171923089037042 0.948423071256426 7 | 6 0.0171923089037042 0.0171923089037042 0.0171923089037042 0.948423071256426 8 | 7 0.17717267398699 0.0878821919687232 0.647062933613719 0.0878821919687232 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M040_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0573908450322538 0.0573908450322538 0.0573908450322538 0.827827466201957 3 | 2 0.968267430564211 0.0105775239209646 0.0105775239209646 0.0105775239209646 4 | 3 0.0105775239209646 0.0105775239209646 0.968267430564211 0.0105775239209646 5 | 4 0.124088616708191 0.103802801091639 0.115982277003152 0.656126307524123 6 | 5 0.436631437390063 0.0105775239209646 0.0105775239209646 0.542213517095112 7 | 6 0.559228530097152 0.0340974027387246 0.372576666012112 0.0340974027387246 8 | 7 0.138156348988225 0.0569421741072173 0.747959299486104 0.0569421741072173 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M052_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.713699488133621 0.0355555534180339 0.21518940745973 0.0355555534180339 3 | 2 0.965895813424702 0.0113680604768995 0.0113680604768995 0.0113680604768995 4 | 3 0.0113680604768995 0.0113680604768995 0.0113680604768995 0.965895813424702 5 | 4 0.0113680604768995 0.597893530121252 0.379370343780351 0.0113680604768995 6 | 5 0.965895813424702 0.0113680604768995 0.0113680604768995 0.0113680604768995 7 | 6 0.603082770670403 0.0359046814182176 0.131204930574251 0.229807612361727 8 | 7 0.301563849153487 0.10922481151179 0.197022425598723 0.392188913915727 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M053_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.130306105130034 0.0387472411984711 0.792199408067195 0.0387472411984711 3 | 2 0.883758271998758 0.0387472411984711 0.0387472411984711 0.0387472411984711 4 | 3 0.701439429612401 0.0387472411984711 0.221066083584827 0.0387472411984711 5 | 4 0.0155360548721029 0.0155360548721029 0.953391841865799 0.0155360548721029 6 | 5 0.0155360548721029 0.0155360548721029 0.953391841865799 0.0155360548721029 7 | 6 0.62637701860711 0.0632800870880896 0.0632800870880896 0.247062814819581 8 | 7 0.577821738594511 0.110334447925345 0.201509366191116 0.110334447925345 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M060_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0128309878415869 0.0128309878415869 0.0128309878415869 0.961507033265198 3 | 2 0.961507033265198 0.0128309878415869 0.0128309878415869 0.0128309878415869 4 | 3 0.961507033265198 0.0128309878415869 0.0128309878415869 0.0128309878415869 5 | 4 0.870529975104672 0.0128309878415869 0.0128309878415869 0.103808046002113 6 | 5 0.891448733086741 0.0361837561504435 0.0361837561504435 0.0361837561504435 7 | 6 0.146749597169589 0.151684195402441 0.641544197520194 0.0600220091127004 8 | 7 0.197361026390237 0.211451922124285 0.481922962920648 0.109264085267187 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M065_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0830920804931059 0.0830920804931059 0.661491291224201 0.172324547975156 3 | 2 0.0372773532630052 0.0372773532630052 0.888167943149015 0.0372773532630052 4 | 3 0.546572640561007 0.0140739705939021 0.425279415406822 0.0140739705939021 5 | 4 0.5035299418691 0.110571994889856 0.0140739705939021 0.371824089802775 6 | 5 0.0140739705939021 0.0140739705939021 0.957778085373927 0.0140739705939021 7 | 6 0.0915673394697202 0.242353562714828 0.652005124377184 0.0140739705939021 8 | 7 0.690610207449128 0.232382661459849 0.0385035636805216 0.0385035636805216 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M068_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.289450300008101 0.105282517644003 0.499984661806897 0.105282517644003 3 | 2 0.616181867785918 0.035201798246505 0.035201798246505 0.313414531801062 4 | 3 0.0116830266815328 0.0116830266815328 0.0116830266815328 0.964950925676011 5 | 4 0.0116830266815328 0.964950925676011 0.0116830266815328 0.0116830266815328 6 | 5 0.964950925676011 0.0116830266815328 0.0116830266815328 0.0116830266815328 7 | 6 0.964950925676011 0.0116830266815328 0.0116830266815328 0.0116830266815328 8 | 7 0.129134650451688 0.0358758509748428 0.799113642056098 0.0358758509748428 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M089_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.941251689404914 0.0195827683623066 0.0195827683623066 0.0195827683623066 3 | 2 0.0195827683623066 0.941251689404914 0.0195827683623066 0.0195827683623066 4 | 3 0.941251689404914 0.0195827683623066 0.0195827683623066 0.0195827683623066 5 | 4 0.112324900353683 0.848509557413538 0.0195827683623066 0.0195827683623066 6 | 5 0.477098537227176 0.112324900353683 0.390993788548669 0.0195827683623066 7 | 6 0.763400416231963 0.107125616758601 0.109891193138963 0.0195827683623066 8 | 7 0.36142408371539 0.270885602322978 0.277204641472513 0.0904856794470277 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M108_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0583238512200205 0.0583238512200205 0.0583238512200205 0.825028447265984 3 | 2 0.0583238512200205 0.0583238512200205 0.0583238512200205 0.825028447265984 4 | 3 0.228364370626413 0.0110649115400709 0.0984863164676124 0.662084404145672 5 | 4 0.116566170466092 0.0110649115400709 0.769064490179748 0.103304430593856 6 | 5 0.0110649115400709 0.0110649115400709 0.19597328654998 0.781896893149646 7 | 6 0.0110649115400709 0.0110649115400709 0.0110649115400709 0.966805268159555 8 | 7 0.057875129204755 0.057875129204755 0.057875129204755 0.826374606955291 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M112_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.033203620572392 0.033203620572392 0.033203620572392 0.900389136949995 3 | 2 0.033203620572392 0.033203620572392 0.033203620572392 0.900389136949995 4 | 3 0.140105128459466 0.00926461540793371 0.0970933467063144 0.753536912824891 5 | 4 0.189910368782207 0.0991473487911722 0.613029783525547 0.0979125022996803 6 | 5 0.00926461540793371 0.00926461540793371 0.292887365456413 0.688583407126326 7 | 6 0.00926461540793371 0.0979125022996803 0.00926461540793371 0.883558270283059 8 | 7 0.0573620387217748 0.0573620387217748 0.1459332565241 0.739342663785825 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M126_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0123065888800001 0.0123065888800001 0.963080231578839 0.0123065888800001 3 | 2 0.0123065888800001 0.0123065888800001 0.963080231578839 0.0123065888800001 4 | 3 0.963080231578839 0.0123065888800001 0.0123065888800001 0.0123065888800001 5 | 4 0.0123065888800001 0.208337964675525 0.66818373124622 0.111171713417094 6 | 5 0.0123065888800001 0.0123065888800001 0.963080231578839 0.0123065888800001 7 | 6 0.292164424975443 0.0123065888800001 0.683222395483396 0.0123065888800001 8 | 7 0.278806175830138 0.255887183477825 0.38318168929901 0.0821249525136268 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M141_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0851134560325405 0.0851134560325405 0.0851134560325405 0.744659628992954 3 | 2 0.0372940434704776 0.0372940434704776 0.888117869425434 0.0372940434704776 4 | 3 0.0128793620934383 0.0128793620934383 0.96136190992779 0.0128793620934383 5 | 4 0.0128793620934383 0.0128793620934383 0.96136190992779 0.0128793620934383 6 | 5 0.219484641829392 0.0367433908141144 0.707028582788509 0.0367433908141144 7 | 6 0.716460514185767 0.0367433908141144 0.210052710432134 0.0367433908141144 8 | 7 0.206192530246528 0.107354887026205 0.197175158881096 0.489277417765494 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M143_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.107772921908759 0.107772921908759 0.193821329216257 0.590632822278716 3 | 2 0.962900946691919 0.0123663508181126 0.0123663508181126 0.0123663508181126 4 | 3 0.0123663508181126 0.0123663508181126 0.0123663508181126 0.962900946691919 5 | 4 0.962900946691919 0.0123663508181126 0.0123663508181126 0.0123663508181126 6 | 5 0.103668114592932 0.109818435597131 0.127039334408889 0.659474114547305 7 | 6 0.756926199326323 0.218341098183708 0.0123663508181126 0.0123663508181126 8 | 7 0.0123663508181126 0.589474826250666 0.385792471259364 0.0123663508181126 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M144_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.26422234159299 0.0828188627958468 0.570139930426155 0.0828188627958468 3 | 2 0.964958655249023 0.0116804468490435 0.0116804468490435 0.0116804468490435 4 | 3 0.964958655249023 0.0116804468490435 0.0116804468490435 0.0116804468490435 5 | 4 0.964958655249023 0.0116804468490435 0.0116804468490435 0.0116804468490435 6 | 5 0.964958655249023 0.0116804468490435 0.0116804468490435 0.0116804468490435 7 | 6 0.0952002235506147 0.800606449822212 0.0116804468490435 0.092512875574283 8 | 7 0.329572513135161 0.549633695541081 0.06039689710485 0.06039689710485 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M153_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.11211003547745 0.575849583428707 0.11211003547745 0.199930349464268 3 | 2 0.0617894991665358 0.146185409259166 0.730235588185672 0.0617894991665358 4 | 3 0.0950240254370463 0.0998166033265825 0.790095736460392 0.0150636395841056 5 | 4 0.870056122313332 0.0998166033265825 0.0150636395841056 0.0150636395841056 6 | 5 0.0150636395841056 0.0998166033265825 0.870056122313332 0.0150636395841056 7 | 6 0.0150636395841056 0.0998166033265825 0.870056122313332 0.0150636395841056 8 | 7 0.444436635457197 0.144544113022402 0.349923495128337 0.0610957577530284 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M156_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.217648333949277 0.125438051273838 0.0343102638228309 0.622603347883168 3 | 2 0.0101956190607588 0.0101956190607588 0.0101956190607588 0.969413144078479 4 | 3 0.0992463255303413 0.0101956190607588 0.0101956190607588 0.880362437608896 5 | 4 0.0101956190607588 0.0101956190607588 0.0101956190607588 0.969413144078479 6 | 5 0.0101956190607588 0.0101956190607588 0.0101956190607588 0.969413144078479 7 | 6 0.0101956190607588 0.0101956190607588 0.106243551038915 0.873365212100323 8 | 7 0.0821831264589834 0.471503209895933 0.184046685791947 0.262266981185982 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M157_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0839638134106351 0.0839638134106351 0.0839638134106351 0.748108561015905 3 | 2 0.0101230245094823 0.0101230245094823 0.880222034440169 0.099531919453341 4 | 3 0.0101230245094823 0.0101230245094823 0.0101230245094823 0.969630929384028 5 | 4 0.0101230245094823 0.0101230245094823 0.772610843868289 0.207143110025222 6 | 5 0.0101230245094823 0.0101230245094823 0.096110077977577 0.883643875915934 7 | 6 0.0101230245094823 0.0101230245094823 0.734305229570154 0.245448724323356 8 | 7 0.0571670668800106 0.0571670668800106 0.228839419569028 0.656826444156097 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M162_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.754943533590485 0.0816854907601892 0.0816854907601892 0.0816854907601892 3 | 2 0.201445824088658 0.0365941808673872 0.72536581120475 0.0365941808673872 4 | 3 0.960027197747161 0.0133242685669419 0.0133242685669419 0.0133242685669419 5 | 4 0.960027197747161 0.0133242685669419 0.0133242685669419 0.0133242685669419 6 | 5 0.960027197747161 0.0133242685669419 0.0133242685669419 0.0133242685669419 7 | 6 0.463978197155205 0.111675242998777 0.196267479390882 0.228079083903123 8 | 7 0.111061796079808 0.18049313004597 0.0133242685669419 0.695120808755268 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M164_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.173860000933686 0.173712287392434 0.0834283668792878 0.568999340182762 3 | 2 0.894004101993321 0.0353319651230926 0.0353319651230926 0.0353319651230926 4 | 3 0.0111466082281208 0.0111466082281208 0.0111466082281208 0.966560174355864 5 | 4 0.966560174355864 0.0111466082281208 0.0111466082281208 0.0111466082281208 6 | 5 0.107702475865125 0.0111466082281208 0.0111466082281208 0.87000430671886 7 | 6 0.798881380268098 0.0349393361289021 0.0349393361289021 0.131239946479399 8 | 7 0.148494989396707 0.246917016009089 0.365980362332842 0.238607636950315 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M176_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.357306105607024 0.0824050576287644 0.477883780986725 0.0824050576287644 3 | 2 0.868569443131593 0.108170637144196 0.0116299572300182 0.0116299572300182 4 | 3 0.0116299572300182 0.102158838231892 0.0116299572300182 0.874581242043898 5 | 4 0.784052361042024 0.0116299572300182 0.0116299572300182 0.192687719233765 6 | 5 0.965110123045771 0.0116299572300182 0.0116299572300182 0.0116299572300182 7 | 6 0.87496910003824 0.0116299572300182 0.0116299572300182 0.101770980237549 8 | 7 0.516879064824388 0.318808278611882 0.0362016621914547 0.128110990255524 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M178_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0603265341719456 0.0603265341719456 0.0603265341719456 0.819020397058174 3 | 2 0.0130412745122818 0.0130412745122818 0.960876174794284 0.0130412745122818 4 | 3 0.0130412745122818 0.0130412745122818 0.0130412745122818 0.960876174794284 5 | 4 0.0130412745122818 0.0130412745122818 0.858392416876179 0.115525032430386 6 | 5 0.202543478392952 0.0130412745122818 0.400628525557848 0.383786719868048 7 | 6 0.0130412745122818 0.0130412745122818 0.478254426039564 0.495663023267001 8 | 7 0.0602729456470117 0.0602729456470117 0.73174716908235 0.147706944715558 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M201_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.517208506195324 0.0584281579562413 0.149860697622706 0.274502638316158 3 | 2 0.283009579937325 0.0107741205624091 0.0107741205624091 0.695442183745009 4 | 3 0.277217905279655 0.0107741205624091 0.0107741205624091 0.701233858402678 5 | 4 0.0979869885939669 0.0107741205624091 0.0996735751701016 0.791565320480675 6 | 5 0.0107741205624091 0.0107741205624091 0.0107741205624091 0.967677643119925 7 | 6 0.0107741205624091 0.0107741205624091 0.0107741205624091 0.967677643119925 8 | 7 0.0107741205624091 0.102569412498937 0.100405490099368 0.786250981646439 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M211_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.269263245195772 0.360668679752099 0.200407187779435 0.169660892208334 3 | 2 0.213352959291671 0.122689609878098 0.0372711867835162 0.626686247401763 4 | 3 0.400966387632203 0.0136592656303455 0.0136592656303455 0.571715083336483 5 | 4 0.19718030858079 0.0136592656303455 0.0136592656303455 0.775501162387897 6 | 5 0.125606572844129 0.798078796351013 0.0381573145628414 0.0381573145628414 7 | 6 0.0381573145628414 0.885528054632301 0.0381573145628414 0.0381573145628414 8 | 7 0.0633641537774895 0.809907540667074 0.0633641537774895 0.0633641537774895 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M227_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.242167906483945 0.538757814116453 0.0620047828924924 0.157069502776823 3 | 2 0.0386394043101561 0.218875523399963 0.0386394043101561 0.703845667851465 4 | 3 0.0153006866458545 0.0153006866458545 0.0153006866458545 0.954097937591383 5 | 4 0.0153006866458545 0.0153006866458545 0.0153006866458545 0.954097937591383 6 | 5 0.0153006866458545 0.109172440256752 0.0153006866458545 0.860226183980486 7 | 6 0.0153006866458545 0.675671270220875 0.0153006866458545 0.293727354016363 8 | 7 0.0620811983914765 0.158058184743783 0.0620811983914765 0.717779421142082 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M228_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.482936162034527 0.211619116050725 0.108073003339822 0.197371726256809 3 | 2 0.0156051531711325 0.670411914976443 0.0156051531711325 0.298377776181234 4 | 3 0.0156051531711325 0.0156051531711325 0.0156051531711325 0.953184537986546 5 | 4 0.106236137797794 0.0156051531711325 0.0156051531711325 0.862553553359885 6 | 5 0.106236137797794 0.0156051531711325 0.0156051531711325 0.862553553359885 7 | 6 0.0388301585568273 0.691174903850627 0.0388301585568273 0.231164778873468 8 | 7 0.0625021928379392 0.162215716981647 0.0625021928379392 0.712779901427627 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M231_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.412365140472584 0.106883253308221 0.106883253308221 0.37386834669602 3 | 2 0.0145252160073923 0.0145252160073923 0.956424355923658 0.0145252160073923 4 | 3 0.0145252160073923 0.956424355923658 0.0145252160073923 0.0145252160073923 5 | 4 0.956424355923658 0.0145252160073923 0.0145252160073923 0.0145252160073923 6 | 5 0.0145252160073923 0.0145252160073923 0.0145252160073923 0.956424355923658 7 | 6 0.0145252160073923 0.0145252160073923 0.956424355923658 0.0145252160073923 8 | 7 0.249670933430663 0.425963331655786 0.163663669644196 0.160702066884987 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M234_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.058576298774632 0.058576298774632 0.824271100768515 0.058576298774632 3 | 2 0.965916638128636 0.0113611203918841 0.0113611203918841 0.0113611203918841 4 | 3 0.0113611203918841 0.0113611203918841 0.0113611203918841 0.965916638128636 5 | 4 0.0113611203918841 0.106357672163184 0.870920086357336 0.0113611203918841 6 | 5 0.965916638128636 0.0113611203918841 0.0113611203918841 0.0113611203918841 7 | 6 0.403021892754883 0.0113611203918841 0.0113611203918841 0.574255865765638 8 | 7 0.270267874182077 0.179710256636807 0.264781306049061 0.285240564788068 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M236_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.262300742380481 0.614345309485022 0.0616769744596801 0.0616769744596801 3 | 2 0.801041303545402 0.125129338890078 0.0369146768168474 0.0369146768168474 4 | 3 0.959536415043032 0.0134878605141575 0.0134878605141575 0.0134878605141575 5 | 4 0.859392416218193 0.0134878605141575 0.0134878605141575 0.113631859338998 6 | 5 0.678817472788046 0.0134878605141575 0.0134878605141575 0.294206802769144 7 | 6 0.687587158505481 0.0134878605141575 0.0134878605141575 0.285437117051709 8 | 7 0.151404906722671 0.0601313472515777 0.55060451193159 0.237859229506601 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M037_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.315547835049928 0.190241985374528 0.212006636214348 0.282203544734165 3 | 2 0.00862191426430533 0.1184004903088 0.86435567860585 0.00862191426430533 4 | 3 0.00862191426430533 0.86435567860585 0.00862191426430533 0.1184004903088 5 | 4 0.00862191426430533 0.00862191426430533 0.00862191426430533 0.974134254650341 6 | 5 0.00862191426430533 0.00862191426430533 0.00862191426430533 0.974134254650341 7 | 6 0.115568019138569 0.0329498996799759 0.818532180692865 0.0329498996799759 8 | 7 0.0563862911776558 0.749437918287827 0.137789501585831 0.0563862911776558 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M046_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.824349987340932 0.0585500035959731 0.0585500035959731 0.0585500035959731 3 | 2 0.0146857902481741 0.955942627034291 0.0146857902481741 0.0146857902481741 4 | 3 0.0146857902481741 0.0146857902481741 0.0146857902481741 0.955942627034291 5 | 4 0.955942627034291 0.0146857902481741 0.0146857902481741 0.0146857902481741 6 | 5 0.955942627034291 0.0146857902481741 0.0146857902481741 0.0146857902481741 7 | 6 0.0146857902481741 0.820842135003972 0.0146857902481741 0.149786282278493 8 | 7 0.411147838945707 0.304972072342184 0.173045744395095 0.110834350817173 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M047_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0802122581797632 0.0802122581797632 0.759363224791154 0.0802122581797632 3 | 2 0.512927721783624 0.0355646809337071 0.0355646809337071 0.415942910609746 4 | 3 0.0122004118712643 0.0122004118712643 0.963398765469714 0.0122004118712643 5 | 4 0.0122004118712643 0.0122004118712643 0.0122004118712643 0.963398765469714 6 | 5 0.963398765469714 0.0122004118712643 0.0122004118712643 0.0122004118712643 7 | 6 0.0122004118712643 0.0122004118712643 0.963398765469714 0.0122004118712643 8 | 7 0.403106039194459 0.0846580151714892 0.163314535620475 0.348921410049221 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M061_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.00613877521514197 0.00613877521514197 0.981583671321393 0.00613877521514197 3 | 2 0.00613877521514197 0.981583671321393 0.00613877521514197 0.00613877521514197 4 | 3 0.100156220736093 0.00613877521514197 0.272747551674364 0.620957449341219 5 | 4 0.00613877521514197 0.00613877521514197 0.981583671321393 0.00613877521514197 6 | 5 0.00613877521514197 0.00613877521514197 0.981583671321393 0.00613877521514197 7 | 6 0.38969380851719 0.368338726115165 0.105647410277269 0.136320057384331 8 | 7 0.189287969587 0.61030959582 0.100201216755256 0.100201216755256 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M069_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.264248555368382 0.0803544562859874 0.0803544562859874 0.575042528672807 3 | 2 0.192828348938255 0.0088111986316702 0.0088111986316702 0.789549256168819 4 | 3 0.0088111986316702 0.0088111986316702 0.973566406475404 0.0088111986316702 5 | 4 0.0088111986316702 0.973566406475404 0.0088111986316702 0.0088111986316702 6 | 5 0.973566406475404 0.0088111986316702 0.0088111986316702 0.0088111986316702 7 | 6 0.0088111986316702 0.973566406475404 0.0088111986316702 0.0088111986316702 8 | 7 0.626482796661044 0.0574420938189306 0.258633011442952 0.0574420938189306 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M075_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.150245179456345 0.0619631097230269 0.0619631097230269 0.725828602003303 3 | 2 0.0148012128291407 0.0148012128291407 0.0148012128291407 0.955596358807824 4 | 3 0.0148012128291407 0.0148012128291407 0.0148012128291407 0.955596358807824 5 | 4 0.0148012128291407 0.0148012128291407 0.0148012128291407 0.955596358807824 6 | 5 0.0148012128291407 0.0148012128291407 0.0148012128291407 0.955596358807824 7 | 6 0.0148012128291407 0.206828780607553 0.204773290079973 0.573596713778579 8 | 7 0.0842994180014102 0.0842994180014102 0.566466532420563 0.264934626698853 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M079_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0328949949438103 0.0328949949438103 0.110439713317493 0.823770296755564 3 | 2 0.120155760980245 0.0328949949438103 0.736509530719129 0.110439713317493 4 | 3 0.00928038287147575 0.00928038287147575 0.00928038287147575 0.972158854139833 5 | 4 0.093880950088104 0.00928038287147575 0.0928381080311065 0.804000561763573 6 | 5 0.00928038287147575 0.00928038287147575 0.874690360827038 0.106748876184269 7 | 6 0.00928038287147575 0.00928038287147575 0.106748876184269 0.874690360827038 8 | 7 0.168134006494198 0.0588521159600198 0.614269790967741 0.15874408552863 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M083_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0992135281373629 0.27347099480322 0.528101949686059 0.0992135281373629 3 | 2 0.135667375608708 0.572736649256284 0.237931945223168 0.0536640282546863 4 | 3 0.82128227785838 0.118722133426168 0.0299977930623292 0.0299977930623292 5 | 4 0.00587389698273713 0.00587389698273713 0.982378308905217 0.00587389698273713 6 | 5 0.00587389698273713 0.982378308905217 0.00587389698273713 0.00587389698273713 7 | 6 0.0306711405156993 0.0306711405156993 0.907986581424143 0.0306711405156993 8 | 7 0.21688422060437 0.564326912258773 0.109394432391795 0.109394432391795 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M101_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0414041836125093 0.0414041836125093 0.0414041836125093 0.875787449874985 3 | 2 0.0191628619443038 0.0191628619443038 0.942511404964335 0.0191628619443038 4 | 3 0.0191628619443038 0.0191628619443038 0.0191628619443038 0.942511404964335 5 | 4 0.942511404964335 0.0191628619443038 0.0191628619443038 0.0191628619443038 6 | 5 0.568835210366727 0.0987753732010476 0.0911521316958989 0.241237275533573 7 | 6 0.235708841315798 0.0638992408272623 0.160988424721921 0.539403485944652 8 | 7 0.0870673571105554 0.0870673571105554 0.0870673571105554 0.738797919622968 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M121_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.687217956011191 0.104260681778464 0.104260681778464 0.104260681778464 3 | 2 0.126713172393486 0.0332115055417226 0.0332115055417226 0.806863818108393 4 | 3 0.00897323442101138 0.973080296524004 0.00897323442101138 0.00897323442101138 5 | 4 0.973080296524004 0.00897323442101138 0.00897323442101138 0.00897323442101138 6 | 5 0.401593613965161 0.00897323442101138 0.202381799194305 0.387051352206563 7 | 6 0.0330258547085456 0.900922438982944 0.0330258547085456 0.0330258547085456 8 | 7 0.181352689301081 0.0810621017003573 0.656523103328498 0.0810621017003573 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M127_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.210756228408445 0.032594193445185 0.032594193445185 0.724055382101676 3 | 2 0.00857090268532809 0.00857090268532809 0.00857090268532809 0.97428729432617 4 | 3 0.132946422892316 0.00857090268532809 0.584140589138782 0.274342087665729 5 | 4 0.293662851838266 0.00857090268532809 0.596293650126067 0.101472597732494 6 | 5 0.00857090268532809 0.00857090268532809 0.100992081317841 0.881866115693661 7 | 6 0.00857090268532809 0.00857090268532809 0.00857090268532809 0.97428729432617 8 | 7 0.0326143621990149 0.0326143621990149 0.0326143621990149 0.902156914244607 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M138_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.506938522476726 0.105484174239702 0.190951212343319 0.196626088135944 3 | 2 0.975066533521372 0.0083111547398715 0.0083111547398715 0.0083111547398715 4 | 3 0.0083111547398715 0.975066533521372 0.0083111547398715 0.0083111547398715 5 | 4 0.0083111547398715 0.0083111547398715 0.0083111547398715 0.975066533521372 6 | 5 0.975066533521372 0.0083111547398715 0.0083111547398715 0.0083111547398715 7 | 6 0.975066533521372 0.0083111547398715 0.0083111547398715 0.0083111547398715 8 | 7 0.0784935950750749 0.0784935950750749 0.764519214399313 0.0784935950750749 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M151_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0557478958883364 0.120904894178528 0.76759931390158 0.0557478958883364 3 | 2 0.0294872868826102 0.0917731362911218 0.849252289881937 0.0294872868826102 4 | 3 0.0991002611617576 0.0697193123163769 0.825350865254305 0.00582956040783162 5 | 4 0.760796001052865 0.0697193123163769 0.0703844246092701 0.0991002611617576 6 | 5 0.00582956040783162 0.0697193123163769 0.812195562809978 0.112255563606083 7 | 6 0.00582956040783162 0.0697193123163769 0.918621566008226 0.00582956040783162 8 | 7 0.136873671758162 0.136239870741706 0.651528619828318 0.0753578360335201 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M154_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0839260428943198 0.0839260428943198 0.748221868906303 0.0839260428943198 3 | 2 0.0320012876579039 0.0320012876579039 0.903996138860931 0.0320012876579039 4 | 3 0.682892651008082 0.00856970229059915 0.29996794629357 0.00856970229059915 5 | 4 0.10141816961188 0.00856970229059915 0.881442427689769 0.00856970229059915 6 | 5 0.0796785053628415 0.0792378364929286 0.832513957736482 0.00856970229059915 7 | 6 0.832374390592383 0.102826922955015 0.0323993435304212 0.0323993435304212 8 | 7 0.200980990252196 0.221259632449877 0.520674697139927 0.0570846760890824 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M169_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.646437224542651 0.0572514445956073 0.239059885156503 0.0572514445956073 3 | 2 0.0100372821798102 0.969888148589857 0.0100372821798102 0.0100372821798102 4 | 3 0.969888148589857 0.0100372821798102 0.0100372821798102 0.0100372821798102 5 | 4 0.185489095946425 0.520360028278535 0.0924052250478029 0.201745645856526 6 | 5 0.759426910859541 0.0100372821798102 0.220498519910126 0.0100372821798102 7 | 6 0.0100372821798102 0.969888148589857 0.0100372821798102 0.0100372821798102 8 | 7 0.969888148589857 0.0100372821798102 0.0100372821798102 0.0100372821798102 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M209_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0803179688343325 0.0803179688343325 0.759046091603668 0.0803179688343325 3 | 2 0.829395041400546 0.0568683181888417 0.0568683181888417 0.0568683181888417 4 | 3 0.122504381812714 0.720551101718016 0.123753048843264 0.0331914635659832 5 | 4 0.00912271518861287 0.00912271518861287 0.876828748745447 0.104925823867293 6 | 5 0.767498687357868 0.00912271518861287 0.214255885254872 0.00912271518861287 7 | 6 0.239530312354965 0.69371809400675 0.0333757965501158 0.0333757965501158 8 | 7 0.451310371203348 0.285091577744513 0.182617629240552 0.0809804206280827 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M229_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.052016740491092 0.052016740491092 0.052016740491092 0.843949779832131 3 | 2 0.102805549540095 0.00655910628766095 0.5882420976174 0.302393245983001 4 | 3 0.00655910628766095 0.00655910628766095 0.00655910628766095 0.980322680565174 5 | 4 0.153198498933737 0.00655910628766095 0.697364307053679 0.14287808715308 6 | 5 0.00655910628766095 0.00655910628766095 0.00655910628766095 0.980322680565174 7 | 6 0.00655910628766095 0.00655910628766095 0.89583522785819 0.0910465589946458 8 | 7 0.0307071205671344 0.0307071205671344 0.0307071205671344 0.90787863735136 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M235_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0816359273329558 0.0816359273329558 0.755092213528939 0.0816359273329558 3 | 2 0.893810170842447 0.0353966095800039 0.0353966095800039 0.0353966095800039 4 | 3 0.0121977675279937 0.0121977675279937 0.0121977675279937 0.963406696013855 5 | 4 0.0121977675279937 0.113626615380734 0.861977848161114 0.0121977675279937 6 | 5 0.963406696013855 0.0121977675279937 0.0121977675279937 0.0121977675279937 7 | 6 0.410159944554373 0.0121977675279937 0.0121977675279937 0.565444518987474 8 | 7 0.257999105027084 0.268210812811982 0.0865105077733343 0.387279577683467 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M012_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0328789423925834 0.796090953786487 0.0328789423925834 0.1381511617227 3 | 2 0.277371950787395 0.218125806732724 0.00894548662494545 0.495556756341827 4 | 3 0.104263170593888 0.0961698533174317 0.00894548662494545 0.790621489950626 5 | 4 0.00894548662494545 0.00894548662494545 0.00894548662494545 0.973163540612057 6 | 5 0.00894548662494545 0.00894548662494545 0.00894548662494545 0.973163540612057 7 | 6 0.00894548662494545 0.00894548662494545 0.00894548662494545 0.973163540612057 8 | 7 0.032709768680212 0.032709768680212 0.214375375899823 0.720205086989861 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M019_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.832591212792457 0.0558029276066798 0.0558029276066798 0.0558029276066798 3 | 2 0.0966226073699798 0.00907801179449789 0.885221367741483 0.00907801179449789 4 | 3 0.972765963316962 0.00907801179449789 0.00907801179449789 0.00907801179449789 5 | 4 0.107870731139151 0.00907801179449789 0.873973243972311 0.00907801179449789 6 | 5 0.88034098346147 0.101502991649992 0.00907801179449789 0.00907801179449789 7 | 6 0.579942318377788 0.208383204944379 0.202596463583794 0.00907801179449789 8 | 7 0.53601577568826 0.261823409655306 0.145620314013802 0.0565404994373066 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M049_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0782916134620316 0.0782916134620316 0.575322791344001 0.268093983595215 3 | 2 0.00573243430648915 0.00573243430648915 0.281233109559675 0.707302024675653 4 | 3 0.00573243430648915 0.00573243430648915 0.982802699928842 0.00573243430648915 5 | 4 0.00573243430648915 0.00573243430648915 0.0896825989751548 0.898852535260172 6 | 5 0.00573243430648915 0.00573243430648915 0.982802699928842 0.00573243430648915 7 | 6 0.00573243430648915 0.106400830546443 0.170013878151255 0.717852859844119 8 | 7 0.052483843781683 0.052483843781683 0.668519089416052 0.226513225131625 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M082_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.881092803283992 0.00966555329802597 0.099576091066395 0.00966555329802597 3 | 2 0.881092803283992 0.00966555329802597 0.099576091066395 0.00966555329802597 4 | 3 0.00966555329802597 0.881092803283992 0.099576091066395 0.00966555329802597 5 | 4 0.971003341052362 0.00966555329802597 0.00966555329802597 0.00966555329802597 6 | 5 0.497567600100071 0.00966555329802597 0.099576091066395 0.393190756481947 7 | 6 0.00966555329802597 0.971003341052362 0.00966555329802597 0.00966555329802597 8 | 7 0.328968086348239 0.105498416396872 0.271539616724664 0.293993876174639 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M086_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.883916226490539 0.0978114800049842 0.00913614513548602 0.00913614513548602 3 | 2 0.285324025457105 0.00913614513548602 0.696403681038419 0.00913614513548602 4 | 3 0.890193241996951 0.00913614513548602 0.0915344644985725 0.00913614513548602 5 | 4 0.100490693940648 0.00913614513548602 0.881237012554875 0.00913614513548602 6 | 5 0.696403681038419 0.00913614513548602 0.285324025457105 0.00913614513548602 7 | 6 0.300576407647989 0.116336330645858 0.573951113337162 0.00913614513548602 8 | 7 0.326935059626775 0.145171417722364 0.494835977834618 0.0330575405590697 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M087_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.90276845135899 0.0324105164148585 0.0324105164148585 0.0324105164148585 3 | 2 0.180600033310772 0.00802618984271389 0.803347585638674 0.00802618984271389 4 | 3 0.975921429106732 0.00802618984271389 0.00802618984271389 0.00802618984271389 5 | 4 0.0966873700510825 0.00802618984271389 0.887260248898367 0.00802618984271389 6 | 5 0.88265139421288 0.00802618984271389 0.101296224736565 0.00802618984271389 7 | 6 0.507476320689529 0.102832509631726 0.381664978470906 0.00802618984271389 8 | 7 0.514301045545382 0.141181048675074 0.312848105256227 0.0316698017686902 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M102_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0330064741348171 0.0330064741348171 0.900980581181854 0.0330064741348171 3 | 2 0.263594053569917 0.00945149550162688 0.717502956598235 0.00945149550162688 4 | 3 0.890570775745253 0.00945149550162688 0.00945149550162688 0.0905262344228984 5 | 4 0.00945149550162688 0.103967999019798 0.762919910171658 0.123660596478323 6 | 5 0.00945149550162688 0.00945149550162688 0.971645514666528 0.00945149550162688 7 | 6 0.762919910171658 0.00945149550162688 0.218177099996493 0.00945149550162688 8 | 7 0.293264286431909 0.373622512763058 0.172299786514308 0.160813417021854 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M109_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0300227815336647 0.114467186132461 0.747741686794613 0.107768346287522 3 | 2 0.00551644019436317 0.81848526323613 0.17048185782414 0.00551644019436317 4 | 3 0.00551644019436317 0.00551644019436317 0.983450680865908 0.00551644019436317 5 | 4 0.00551644019436317 0.892973140112296 0.095993980947977 0.00551644019436317 6 | 5 0.00551644019436317 0.095993980947977 0.892973140112296 0.00551644019436317 7 | 6 0.00551644019436317 0.306348197099141 0.604919930841029 0.0832154333144664 8 | 7 0.0791479336941687 0.0791479336941687 0.762556200279509 0.0791479336941687 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M120_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0552279862528441 0.0552279862528441 0.44783142772478 0.441712600886907 3 | 2 0.00614270661056647 0.00614270661056647 0.00614270661056647 0.981571881781228 4 | 3 0.00614270661056647 0.00614270661056647 0.00614270661056647 0.981571881781228 5 | 4 0.00614270661056647 0.00614270661056647 0.00614270661056647 0.981571881781228 6 | 5 0.0303420914461716 0.0303420914461716 0.713695314995554 0.225620504932692 7 | 6 0.0542086549923028 0.0542086549923028 0.558207751982341 0.333374939580978 8 | 7 0.0783654510765548 0.0783654510765548 0.66704959375107 0.176219506224702 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M146_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.757581138093524 0.0808062882916104 0.0808062882916104 0.0808062882916104 3 | 2 0.326151017023304 0.123042401487181 0.518076580241003 0.032730004207642 4 | 3 0.974428180192358 0.00852393919768473 0.00852393919768473 0.00852393919768473 5 | 4 0.974428180192358 0.00852393919768473 0.00852393919768473 0.00852393919768473 6 | 5 0.974428180192358 0.00852393919768473 0.00852393919768473 0.00852393919768473 7 | 6 0.772857397359491 0.119943631515674 0.098675029712564 0.00852393919768473 8 | 7 0.6872890442497 0.203573134184849 0.00852393919768473 0.10061388015318 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M160_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.798664692158047 0.0339552528238548 0.0339552528238548 0.133424804590437 3 | 2 0.00974615106707635 0.00974615106707635 0.00974615106707635 0.970761549092077 4 | 3 0.884217686096699 0.00974615106707635 0.00974615106707635 0.0962900140624551 5 | 4 0.970761549092077 0.00974615106707635 0.00974615106707635 0.00974615106707635 6 | 5 0.878450315964202 0.00974615106707635 0.00974615106707635 0.102057384194952 7 | 6 0.899438906606131 0.033520364762217 0.033520364762217 0.033520364762217 8 | 7 0.286278996544742 0.195872427396893 0.413269602673414 0.104578972504055 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M232_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.00988973714483012 0.113670611300259 0.107291232460311 0.769148420297064 3 | 2 0.00988973714483012 0.00988973714483012 0.00988973714483012 0.970330789767973 4 | 3 0.107238070969978 0.00988973714483012 0.00988973714483012 0.872982455942825 5 | 4 0.0961095989936245 0.00988973714483012 0.0964640089291772 0.797536656134831 6 | 5 0.00988973714483012 0.00988973714483012 0.0950463691869666 0.885174157725837 7 | 6 0.00988973714483012 0.100592884678366 0.0950463691869666 0.794471010192301 8 | 7 0.00988973714483012 0.103463605156342 0.195407187464312 0.691239471436978 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M238_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.105615045950549 0.105615045950549 0.584614327189364 0.204155582548799 3 | 2 0.293411735905703 0.00968730268478072 0.00968730268478072 0.687213654307496 4 | 3 0.00968730268478072 0.00968730268478072 0.970938087528418 0.00968730268478072 5 | 4 0.00968730268478072 0.00968730268478072 0.00968730268478072 0.970938087528418 6 | 5 0.00968730268478072 0.00968730268478072 0.880722980439519 0.0999024097736798 7 | 6 0.00968730268478072 0.00968730268478072 0.0999836464938924 0.880641743719307 8 | 7 0.123243996941939 0.0335089661174179 0.720083767821391 0.12316326521699 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M001_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.39532879396435 0.105513888686126 0.105513888686126 0.393643427745405 3 | 2 0.00770456803068082 0.00770456803068082 0.00770456803068082 0.976886297348457 4 | 3 0.976886297348457 0.00770456803068082 0.00770456803068082 0.00770456803068082 5 | 4 0.976886297348457 0.00770456803068082 0.00770456803068082 0.00770456803068082 6 | 5 0.00770456803068082 0.00770456803068082 0.00770456803068082 0.976886297348457 7 | 6 0.00770456803068082 0.00770456803068082 0.00770456803068082 0.976886297348457 8 | 7 0.321131137484576 0.143803698114993 0.478370946765367 0.0566942181612342 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M002_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.773202708628553 0.0755990967724702 0.0755990967724702 0.0755990967724702 3 | 2 0.00430461221593073 0.00430461221593073 0.987086161345983 0.00430461221593073 4 | 3 0.987086161345983 0.00430461221593073 0.00430461221593073 0.00430461221593073 5 | 4 0.00430461221593073 0.987086161345983 0.00430461221593073 0.00430461221593073 6 | 5 0.00430461221593073 0.00430461221593073 0.987086161345983 0.00430461221593073 7 | 6 0.228809755236608 0.10208869663005 0.00430461221593073 0.664796933911185 8 | 7 0.427754153606094 0.0793093155884373 0.0997300686202917 0.393206460178951 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M008_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.976645202675335 0.00778493118669669 0.00778493118669669 0.00778493118669669 3 | 2 0.0979710760793953 0.685620461005767 0.208623527963562 0.00778493118669669 4 | 3 0.976645202675335 0.00778493118669669 0.00778493118669669 0.00778493118669669 5 | 4 0.101571012814051 0.882859121047973 0.00778493118669669 0.00778493118669669 6 | 5 0.976645202675335 0.00778493118669669 0.00778493118669669 0.00778493118669669 7 | 6 0.293509765996908 0.200390339320415 0.102470996997715 0.403628893920384 8 | 7 0.667790528533357 0.0798585093492451 0.0798585093492451 0.172492453814989 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M022_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.268221312682607 0.0829313540793576 0.272138394820678 0.376708940945804 3 | 2 0.00960823913423693 0.00960823913423693 0.00960823913423693 0.971175286760165 4 | 3 0.971175286760165 0.00960823913423693 0.00960823913423693 0.00960823913423693 5 | 4 0.00960823913423693 0.00960823913423693 0.971175286760165 0.00960823913423693 6 | 5 0.00960823913423693 0.00960823913423693 0.971175286760165 0.00960823913423693 7 | 6 0.00960823913423693 0.00960823913423693 0.877684300946812 0.103099224947591 8 | 7 0.591091834175316 0.10395683684393 0.10395683684393 0.200994489206751 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M025_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.56581046380828 0.184580241664291 0.080343963638578 0.169265330645431 3 | 2 0.00615312633272871 0.00615312633272871 0.00615312633272871 0.981540621551337 4 | 3 0.00615312633272871 0.00615312633272871 0.00615312633272871 0.981540621551337 5 | 4 0.00615312633272871 0.00615312633272871 0.00615312633272871 0.981540621551337 6 | 5 0.00615312633272871 0.00615312633272871 0.00615312633272871 0.981540621551337 7 | 6 0.00615312633272871 0.00615312633272871 0.00615312633272871 0.981540621551337 8 | 7 0.0545680904020458 0.147523892443351 0.272217299111428 0.52569071776952 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M031_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.00647952351346512 0.00647952351346512 0.00647952351346512 0.980561431632273 3 | 2 0.00647952351346512 0.00647952351346512 0.00647952351346512 0.980561431632273 4 | 3 0.536437275324277 0.00647952351346512 0.177269807570215 0.279813395764714 5 | 4 0.0879178724305586 0.00647952351346512 0.185654273257177 0.719948332971471 6 | 5 0.00647952351346512 0.00647952351346512 0.00647952351346512 0.980561431632273 7 | 6 0.00647952351346512 0.00647952351346512 0.00647952351346512 0.980561431632273 8 | 7 0.0569500736473458 0.14372969379225 0.143649910538235 0.655670322989179 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M050_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0547719353224411 0.0547719353224411 0.835684192517964 0.0547719353224411 3 | 2 0.00643115088969442 0.980706548549774 0.00643115088969442 0.00643115088969442 4 | 3 0.00643115088969442 0.00643115088969442 0.980706548549774 0.00643115088969442 5 | 4 0.00643115088969442 0.893047559738362 0.0940901397011093 0.00643115088969442 6 | 5 0.00643115088969442 0.0940901397011093 0.893047559738362 0.00643115088969442 7 | 6 0.00643115088969442 0.22171430864045 0.678504736348866 0.0933498053398482 8 | 7 0.0564697130878233 0.234661253699658 0.57065072017103 0.138218311454527 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M051_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.446003404503079 0.0566725164453121 0.0566725164453121 0.440651566392308 3 | 2 0.00901702888447405 0.00901702888447405 0.00901702888447405 0.972948908920515 4 | 3 0.972948908920515 0.00901702888447405 0.00901702888447405 0.00901702888447405 5 | 4 0.00901702888447405 0.972948908920515 0.00901702888447405 0.00901702888447405 6 | 5 0.58286539702691 0.00901702888447405 0.00901702888447405 0.399100540778078 7 | 6 0.00901702888447405 0.00901702888447405 0.00901702888447405 0.972948908920515 8 | 7 0.104460301246234 0.104460301246234 0.194732176924498 0.596347218686662 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M062_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.757020210373493 0.0809932638995346 0.0809932638995346 0.0809932638995346 3 | 2 0.327083213502225 0.123145388733561 0.516828233031373 0.0329431610349821 4 | 3 0.973795858185309 0.00873471488222294 0.00873471488222294 0.00873471488222294 5 | 4 0.973795858185309 0.00873471488222294 0.00873471488222294 0.00873471488222294 6 | 5 0.973795858185309 0.00873471488222294 0.00873471488222294 0.00873471488222294 7 | 6 0.772119715626907 0.120614436205739 0.0985311361171097 0.00873471488222294 8 | 7 0.687405478522006 0.203937122894097 0.00873471488222294 0.0999226865336534 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M077_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.134653715333477 0.130355700786008 0.0534142563094468 0.681576325475596 3 | 2 0.00575932442110899 0.00575932442110899 0.00575932442110899 0.982722029586617 4 | 3 0.00575932442110899 0.00575932442110899 0.00575932442110899 0.982722029586617 5 | 4 0.00575932442110899 0.00575932442110899 0.00575932442110899 0.982722029586617 6 | 5 0.00575932442110899 0.0980410203842298 0.00575932442110899 0.890440333623496 7 | 6 0.00575932442110899 0.327792013557418 0.00575932442110899 0.660689340450305 8 | 7 0.0529684847636527 0.717499156470496 0.0529684847636527 0.176563873547152 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M078_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.121621519159828 0.131334387257883 0.053033484273035 0.694010606634789 3 | 2 0.00757788839760344 0.00757788839760344 0.00757788839760344 0.977266337552181 4 | 3 0.00757788839760344 0.00757788839760344 0.00757788839760344 0.977266337552181 5 | 4 0.00757788839760344 0.00757788839760344 0.00757788839760344 0.977266337552181 6 | 5 0.00757788839760344 0.174909139452995 0.00757788839760344 0.809935086496792 7 | 6 0.00757788839760344 0.281986843843568 0.00757788839760344 0.702857382106218 8 | 7 0.0997295664524362 0.506920936974146 0.0997295664524362 0.293619931784842 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M081_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.97986256700864 0.00671247789631372 0.00671247789631372 0.00671247789631372 3 | 2 0.829912227345672 0.156662817559278 0.00671247789631372 0.00671247789631372 4 | 3 0.00671247789631372 0.97986256700864 0.00671247789631372 0.00671247789631372 5 | 4 0.97986256700864 0.00671247789631372 0.00671247789631372 0.00671247789631372 6 | 5 0.0772643138116462 0.133262691177024 0.00671247789631372 0.782760517812594 7 | 6 0.00671247789631372 0.97986256700864 0.00671247789631372 0.00671247789631372 8 | 7 0.492456365143676 0.153979898203796 0.171614806337828 0.181948931706103 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M088_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.907615942809972 0.0307946867034003 0.0307946867034003 0.0307946867034003 3 | 2 0.00680539940661136 0.00680539940661136 0.979583800478626 0.00680539940661136 4 | 3 0.979583800478626 0.00680539940661136 0.00680539940661136 0.00680539940661136 5 | 4 0.0812995256756354 0.00680539940661136 0.905089674209599 0.00680539940661136 6 | 5 0.979583800478626 0.00680539940661136 0.00680539940661136 0.00680539940661136 7 | 6 0.531303420531282 0.285003653646033 0.176887525114532 0.00680539940661136 8 | 7 0.520756483946346 0.219657975133003 0.17321649193856 0.0863690476805494 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M097_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.00452161562191429 0.00452161562191429 0.00452161562191429 0.98643515326452 3 | 2 0.00452161562191429 0.00452161562191429 0.98643515326452 0.00452161562191429 4 | 3 0.00452161562191429 0.00452161562191429 0.00452161562191429 0.98643515326452 5 | 4 0.98643515326452 0.00452161562191429 0.00452161562191429 0.00452161562191429 6 | 5 0.237831329776797 0.570591103929389 0.0694680305322832 0.122109535891793 7 | 6 0.98643515326452 0.00452161562191429 0.00452161562191429 0.00452161562191429 8 | 7 0.0968727977606325 0.0968727977606325 0.455645420609172 0.350608983763122 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M099_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.00485402999821605 0.00485402999821605 0.00485402999821605 0.985437910116276 3 | 2 0.00485402999821605 0.00485402999821605 0.985437910116276 0.00485402999821605 4 | 3 0.00485402999821605 0.00485402999821605 0.00485402999821605 0.985437910116276 5 | 4 0.985437910116276 0.00485402999821605 0.00485402999821605 0.00485402999821605 6 | 5 0.508925566275392 0.376992181596303 0.00485402999821605 0.109228222241011 7 | 6 0.60169479855361 0.0514230142433938 0.213556979754813 0.133325207547692 8 | 7 0.0965629792229204 0.0965629792229204 0.360972719315262 0.445901320445929 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M100_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.00532654892926832 0.00532654892926832 0.00532654892926832 0.984020355612855 3 | 2 0.00532654892926832 0.00532654892926832 0.984020355612855 0.00532654892926832 4 | 3 0.00532654892926832 0.00532654892926832 0.00532654892926832 0.984020355612855 5 | 4 0.984020355612855 0.00532654892926832 0.00532654892926832 0.00532654892926832 6 | 5 0.490412049605043 0.404247756329616 0.00532654892926832 0.100013647536734 7 | 6 0.673455273144498 0.0515738524030351 0.13470839732293 0.140262476581875 8 | 7 0.0963701262022087 0.0963701262022087 0.355212010711824 0.452047738640522 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M103_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.00965532451511902 0.00965532451511902 0.971034031170204 0.00965532451511902 3 | 2 0.186153135273642 0.00965532451511902 0.794536220411681 0.00965532451511902 4 | 3 0.971034031170204 0.00965532451511902 0.00965532451511902 0.00965532451511902 5 | 4 0.00965532451511902 0.106559739752812 0.763391151979633 0.120393788467996 6 | 5 0.00965532451511902 0.00965532451511902 0.971034031170204 0.00965532451511902 7 | 6 0.763391151979633 0.00965532451511902 0.217298203705689 0.00965532451511902 8 | 7 0.312983970753302 0.308198301974468 0.192780278674256 0.186037445632929 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M104_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0328371276042897 0.0328371276042897 0.901488620102929 0.0328371276042897 3 | 2 0.00925910296903044 0.00925910296903044 0.972222694531267 0.00925910296903044 4 | 3 0.972222694531267 0.00925910296903044 0.00925910296903044 0.00925910296903044 5 | 4 0.00925910296903044 0.197243057618107 0.686305926944115 0.107191915907109 6 | 5 0.00925910296903044 0.00925910296903044 0.972222694531267 0.00925910296903044 7 | 6 0.590513369503245 0.00925910296903044 0.390968427997055 0.00925910296903044 8 | 7 0.360908628119485 0.190569154572861 0.367942102370767 0.0805801124217138 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M105_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0322045160464388 0.0322045160464388 0.903386454402843 0.0322045160464388 3 | 2 0.00863687553219887 0.00863687553219887 0.974089375176424 0.00863687553219887 4 | 3 0.974089375176424 0.00863687553219887 0.00863687553219887 0.00863687553219887 5 | 4 0.00863687553219887 0.193047176377405 0.689072028916931 0.109243920946485 6 | 5 0.00863687553219887 0.00863687553219887 0.974089375176424 0.00863687553219887 7 | 6 0.591164699843775 0.00863687553219887 0.391561550864848 0.00863687553219887 8 | 7 0.365814774758368 0.271332870453425 0.282574184832671 0.0802781663642895 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M111_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.906348608959452 0.0312171297914893 0.0312171297914893 0.0312171297914893 3 | 2 0.753416547466716 0.231325744070362 0.00762885242361852 0.00762885242361852 4 | 3 0.00762885242361852 0.977113439113457 0.00762885242361852 0.00762885242361852 5 | 4 0.977113439113457 0.00762885242361852 0.00762885242361852 0.00762885242361852 6 | 5 0.00762885242361852 0.192342019516062 0.00762885242361852 0.792400272021014 7 | 6 0.00762885242361852 0.977113439113457 0.00762885242361852 0.00762885242361852 8 | 7 0.546032838368432 0.0581726967114643 0.230545965203325 0.165248499377502 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M113_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.790790772967245 0.069736408567501 0.069736408567501 0.069736408567501 3 | 2 0.00388111803242964 0.988356645330312 0.00388111803242964 0.00388111803242964 4 | 3 0.00388111803242964 0.00388111803242964 0.00388111803242964 0.988356645330312 5 | 4 0.988356645330312 0.00388111803242964 0.00388111803242964 0.00388111803242964 6 | 5 0.988356645330312 0.00388111803242964 0.00388111803242964 0.00388111803242964 7 | 6 0.00388111803242964 0.988356645330312 0.00388111803242964 0.00388111803242964 8 | 7 0.432036802900221 0.294945818273152 0.169992751280551 0.103024627770002 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M117_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0796240434418326 0.0796240434418326 0.591073984618945 0.249677927402265 3 | 2 0.00481514179504364 0.00481514179504364 0.0822664633154859 0.908103252025239 4 | 3 0.00481514179504364 0.00481514179504364 0.898475938875073 0.0918937764656516 5 | 4 0.00481514179504364 0.00481514179504364 0.700167866831442 0.290201848509283 6 | 5 0.00481514179504364 0.00481514179504364 0.0791857231074331 0.911183992233292 7 | 6 0.00481514179504364 0.00481514179504364 0.985554573545681 0.00481514179504364 8 | 7 0.0293187887765079 0.0293187887765079 0.116353373541885 0.825009049886946 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M124_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0301900713859373 0.0301900713859373 0.0301900713859373 0.909429784859157 3 | 2 0.00629948179958758 0.00629948179958758 0.00629948179958758 0.981101553823232 4 | 3 0.224776911745509 0.00629948179958758 0.184026869134536 0.584896736542362 5 | 4 0.208458455767811 0.103202550389408 0.483070472759271 0.205268520305505 6 | 5 0.00629948179958758 0.00629948179958758 0.791683882770927 0.195717152851891 7 | 6 0.00629948179958758 0.00629948179958758 0.00629948179958758 0.981101553823232 8 | 7 0.00629948179958758 0.00629948179958758 0.00629948179958758 0.981101553823232 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M142_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.762509870175323 0.0791633768215905 0.0791633768215905 0.0791633768215905 3 | 2 0.974051961825069 0.00864934515937539 0.00864934515937539 0.00864934515937539 4 | 3 0.00864934515937539 0.974051961825069 0.00864934515937539 0.00864934515937539 5 | 4 0.00864934515937539 0.00864934515937539 0.00864934515937539 0.974051961825069 6 | 5 0.974051961825069 0.00864934515937539 0.00864934515937539 0.00864934515937539 7 | 6 0.521991671568225 0.317983267747242 0.0325968476589352 0.127428216292518 8 | 7 0.104219040959224 0.104219040959224 0.687342879365605 0.104219040959224 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M147_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.0289260721554996 0.168882979546732 0.773264876772799 0.0289260721554996 3 | 2 0.984561125294953 0.00514629085692418 0.00514629085692418 0.00514629085692418 4 | 3 0.00514629085692418 0.914510454247717 0.075196961904161 0.00514629085692418 5 | 4 0.984561125294953 0.00514629085692418 0.00514629085692418 0.00514629085692418 6 | 5 0.00514629085692418 0.184167701849805 0.805539714302068 0.00514629085692418 7 | 6 0.984561125294953 0.00514629085692418 0.00514629085692418 0.00514629085692418 8 | 7 0.301008210512597 0.184126594839406 0.209704356603704 0.305160835363742 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M148_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.974659063714268 0.00844697756161774 0.00844697756161774 0.00844697756161774 3 | 2 0.283085945567195 0.00844697756161774 0.70002009570869 0.00844697756161774 4 | 3 0.974659063714268 0.00844697756161774 0.00844697756161774 0.00844697756161774 5 | 4 0.974659063714268 0.00844697756161774 0.00844697756161774 0.00844697756161774 6 | 5 0.193759322124929 0.0955764367951483 0.702217259917426 0.00844697756161774 7 | 6 0.974659063714268 0.00844697756161774 0.00844697756161774 0.00844697756161774 8 | 7 0.224875901129375 0.312169586293529 0.225891494291442 0.23706301907418 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M149_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.169792511215775 0.45246912127402 0.164509463052899 0.213228903790404 3 | 2 0.0969297458225215 0.0919880574446695 0.00658218974642937 0.804500007214712 4 | 3 0.00658218974642937 0.00658218974642937 0.00658218974642937 0.980253430989041 5 | 4 0.00658218974642937 0.00658218974642937 0.00658218974642937 0.980253430989041 6 | 5 0.00658218974642937 0.00658218974642937 0.00658218974642937 0.980253430989041 7 | 6 0.00658218974642937 0.00658218974642937 0.0905657264724462 0.896269894263026 8 | 7 0.0305356185277595 0.0305356185277595 0.0305356185277595 0.908393145775856 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M150_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.120423343332728 0.0303640190993599 0.0303640190993599 0.818848617321133 3 | 2 0.00604678406505991 0.00604678406505991 0.00604678406505991 0.981859645996802 4 | 3 0.00604678406505991 0.00604678406505991 0.00604678406505991 0.981859645996802 5 | 4 0.00604678406505991 0.00604678406505991 0.00604678406505991 0.981859645996802 6 | 5 0.00604678406505991 0.00604678406505991 0.00604678406505991 0.981859645996802 7 | 6 0.00604678406505991 0.093329554441326 0.0951580423584172 0.805465617327178 8 | 7 0.0784562340543257 0.174053246759709 0.551652053306899 0.195838467666167 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M158_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.539994101908106 0.1802351520845 0.0797502721051169 0.200020472182598 3 | 2 0.00531105731434936 0.00531105731434936 0.00531105731434936 0.984066826153735 4 | 3 0.00531105731434936 0.00531105731434936 0.00531105731434936 0.984066826153735 5 | 4 0.00531105731434936 0.00531105731434936 0.00531105731434936 0.984066826153735 6 | 5 0.00531105731434936 0.00531105731434936 0.00531105731434936 0.984066826153735 7 | 6 0.00531105731434936 0.00531105731434936 0.00531105731434936 0.984066826153735 8 | 7 0.0532406055196184 0.131116830321795 0.255009599024897 0.560632966996189 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M170_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.268546603675054 0.0794929450336221 0.0794929450336221 0.572467507324113 3 | 2 0.00924450767852043 0.00924450767852043 0.97226647443589 0.00924450767852043 4 | 3 0.0971392799523235 0.00924450767852043 0.00924450767852043 0.884371702162086 5 | 4 0.00924450767852043 0.00924450767852043 0.97226647443589 0.00924450767852043 6 | 5 0.00924450767852043 0.00924450767852043 0.00924450767852043 0.97226647443589 7 | 6 0.00924450767852043 0.00924450767852043 0.97226647443589 0.00924450767852043 8 | 7 0.547425367691711 0.0831238383985125 0.183887509798094 0.185563286833778 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M045_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.00346394742913858 0.00346394742913858 0.00346394742913858 0.989608158696647 3 | 2 0.00346394742913858 0.00346394742913858 0.989608158696647 0.00346394742913858 4 | 3 0.00346394742913858 0.00346394742913858 0.00346394742913858 0.989608158696647 5 | 4 0.989608158696647 0.00346394742913858 0.00346394742913858 0.00346394742913858 6 | 5 0.183345408144104 0.565190610620191 0.0655315907474171 0.18593239147235 7 | 6 0.989608158696647 0.00346394742913858 0.00346394742913858 0.00346394742913858 8 | 7 0.0917993560325941 0.0917993560325941 0.410145394567985 0.406255893298404 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M098_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.00840053248287238 0.00840053248287238 0.00840053248287238 0.974798402710077 3 | 2 0.00840053248287238 0.00840053248287238 0.974798402710077 0.00840053248287238 4 | 3 0.00840053248287238 0.00840053248287238 0.00840053248287238 0.974798402710077 5 | 4 0.974798402710077 0.00840053248287238 0.00840053248287238 0.00840053248287238 6 | 5 0.0906398411419586 0.565045114484495 0.0612936547216357 0.283021389810602 7 | 6 0.974798402710077 0.00840053248287238 0.00840053248287238 0.00840053248287238 8 | 7 0.0945728433050756 0.0945728433050756 0.437142472082549 0.373711841752717 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M195_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.237426318753996 0.199675622952797 0.252356050872447 0.310542009161303 3 | 2 0.00347657619933987 0.940044409275546 0.00347657619933987 0.0530024372070121 4 | 3 0.989570270283218 0.00347657619933987 0.00347657619933987 0.00347657619933987 5 | 4 0.989570270283218 0.00347657619933987 0.00347657619933987 0.00347657619933987 6 | 5 0.989570270283218 0.00347657619933987 0.00347657619933987 0.00347657619933987 7 | 6 0.989570270283218 0.00347657619933987 0.00347657619933987 0.00347657619933987 8 | 7 0.0268564596600667 0.0268564596600667 0.919430619793634 0.0268564596600667 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M244_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.180382251687496 0.0836396163340251 0.460564065407278 0.275414067355236 3 | 2 0.00804004663612971 0.00804004663612971 0.00804004663612971 0.975879860152032 4 | 3 0.975879860152032 0.00804004663612971 0.00804004663612971 0.00804004663612971 5 | 4 0.975879860152032 0.00804004663612971 0.00804004663612971 0.00804004663612971 6 | 5 0.00804004663612971 0.00804004663612971 0.00804004663612971 0.975879860152032 7 | 6 0.00804004663612971 0.00804004663612971 0.00804004663612971 0.975879860152032 8 | 7 0.164369247550741 0.263167659660029 0.493206615753498 0.0792564761975087 9 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M351_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.55555555555556 0.11111111111111 0.11111111111111 0.22222222222222 3 | 2 0.22222222222222 0 0.55555555555556 0.22222222222222 4 | 3 0.027777777777778 0 0.94444444444444 0.027777777777778 5 | 4 0.97222222222222 0.027777777777778 0 0 6 | 5 0.055555555555556 0.91666666666667 0.027777777777778 0 7 | 6 0.55555555555556 0 0.38888888888889 0.055555555555556 8 | 7 0.27777777777778 0 0.69444444444444 0.027777777777778 9 | 8 0.94444444444444 0.027777777777778 0.027777777777778 0 10 | 9 0.22222222222222 0.055555555555556 0.72222222222222 0 11 | 10 0 0.97222222222222 0 0.027777777777778 12 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M074_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.323700271419175 0.129601294234235 0.222720113745929 0.323978325180516 3 | 2 0.010278288780035 0.010278288780035 0.969165130453199 0.010278288780035 4 | 3 0.782535336692567 0.010278288780035 0.108149347573729 0.0990370237469724 5 | 4 0.969165130453199 0.010278288780035 0.010278288780035 0.010278288780035 6 | 5 0.010278288780035 0.010278288780035 0.010278288780035 0.969165130453199 7 | 6 0.010278288780035 0.010278288780035 0.969165130453199 0.010278288780035 8 | 7 0.63731459035423 0.058421634695811 0.148502516294399 0.155761259549747 9 | 8 0.310646439026569 0.130681477886001 0.334146647175505 0.2245254351749 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M331_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.7906976744186 0.13953488372093 0.023255813953488 0.046511627906977 3 | 2 0.069767441860465 0.023255813953488 0.83720930232558 0.069767441860465 4 | 3 0.93023255813953 0.069767441860465 0 0 5 | 4 0 0.97674418604651 0 0.023255813953488 6 | 5 0.13953488372093 0.023255813953488 0.3953488372093 0.44186046511628 7 | 6 0.95348837209302 0.023255813953488 0 0.023255813953488 8 | 7 0 0.88372093023256 0.046511627906977 0.069767441860465 9 | 8 0.11627906976744 0 0.88372093023256 0 10 | 9 0.72093023255814 0.11627906976744 0 0.16279069767442 11 | 10 0.069767441860465 0.2093023255814 0.13953488372093 0.58139534883721 12 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M033_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.212203224238528 0.129282764199032 0.529231249046511 0.129282764199032 3 | 2 0.96976571513663 0.0100780952609581 0.0100780952609581 0.0100780952609581 4 | 3 0.0100780952609581 0.0100780952609581 0.0100780952609581 0.96976571513663 5 | 4 0.96976571513663 0.0100780952609581 0.0100780952609581 0.0100780952609581 6 | 5 0.96976571513663 0.0100780952609581 0.0100780952609581 0.0100780952609581 7 | 6 0.96976571513663 0.0100780952609581 0.0100780952609581 0.0100780952609581 8 | 7 0.211219159369854 0.530113980770901 0.224001732798915 0.0346651229530925 9 | 8 0.233726327673742 0.314652487290389 0.320816953549209 0.130804231633577 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M070_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.607397525564136 0.130867491829291 0.130867491829291 0.130867491829291 3 | 2 0.0164197322293056 0.0164197322293056 0.950740800258744 0.0164197322293056 4 | 3 0.0164197322293056 0.0164197322293056 0.950740800258744 0.0164197322293056 5 | 4 0.85971495944523 0.0164197322293056 0.0164197322293056 0.10744557304282 6 | 5 0.0164197322293056 0.0164197322293056 0.950740800258744 0.0164197322293056 7 | 6 0.582607237810568 0.0164197322293056 0.10519340290493 0.295779624001857 8 | 7 0.304847572188622 0.0164197322293056 0.389709578940544 0.289023113588187 9 | 8 0.320765806805383 0.135637619297764 0.407958947290758 0.135637619297764 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M106_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.328310090142541 0.407810043482976 0.131939932564949 0.131939932564949 3 | 2 0.897566337024074 0.034144555969364 0.034144555969364 0.034144555969364 4 | 3 0.0101575478330609 0.0101575478330609 0.969527360979772 0.0101575478330609 5 | 4 0.0101575478330609 0.0101575478330609 0.969527360979772 0.0101575478330609 6 | 5 0.969527360979772 0.0101575478330609 0.0101575478330609 0.0101575478330609 7 | 6 0.0576934479119749 0.630209308284194 0.165632566258594 0.14646467730971 8 | 7 0.649822554246116 0.188223937559225 0.0809767527389904 0.0809767527389904 9 | 8 0.339070646505922 0.313697725478643 0.218962235940942 0.128269392101506 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M122_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.522103438857505 0.131798946798685 0.131798946798685 0.214298669224611 3 | 2 0.0625411033390471 0.0625411033390471 0.812376692659747 0.0625411033390471 4 | 3 0.710227383551784 0.0395577957708748 0.122693855728054 0.127520963956956 5 | 4 0.195493938585509 0.0162832395264046 0.771939584159448 0.0162832395264046 6 | 5 0.190298424233204 0.0162832395264046 0.0996234099840597 0.693794928054097 7 | 6 0.597975335867867 0.0162832395264046 0.182454216289528 0.203287210113965 8 | 7 0.282501530938907 0.0996234099840597 0.0162832395264046 0.601591821348394 9 | 8 0.423025226947877 0.134511931116575 0.307950912737451 0.134511931116575 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M134_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.206403820506 0.132411499433526 0.528773179422357 0.132411499433526 3 | 2 0.814857780510373 0.0617140753301687 0.0617140753301687 0.0617140753301687 4 | 3 0.0386579227620593 0.0386579227620593 0.0386579227620593 0.884026234368706 5 | 4 0.0386579227620593 0.884026234368706 0.0386579227620593 0.0386579227620593 6 | 5 0.952347055177715 0.0158843126448898 0.0158843126448898 0.0158843126448898 7 | 6 0.549829895835287 0.169622536733794 0.0930279201443293 0.187519640398973 8 | 7 0.0623677957386528 0.0623677957386528 0.812896611487199 0.0623677957386528 9 | 8 0.522114735493788 0.210931099685134 0.133477084076465 0.133477084076465 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M152_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.59461678301494 0.135127740080643 0.135127740080643 0.135127740080643 3 | 2 0.883468603472907 0.0388437981172282 0.0388437981172282 0.0388437981172282 4 | 3 0.0156043133130774 0.377852649233234 0.0156043133130774 0.590938720590541 5 | 4 0.0156043133130774 0.0156043133130774 0.953187056510698 0.0156043133130774 6 | 5 0.862000244280145 0.0156043133130774 0.10679112554363 0.0156043133130774 7 | 6 0.10679112554363 0.862000244280145 0.0156043133130774 0.0156043133130774 8 | 7 0.586908215748519 0.0156043133130774 0.381883154075256 0.0156043133130774 9 | 8 0.608334201725063 0.130555267829521 0.130555267829521 0.130555267829521 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M188_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.226245598263304 0.417081013610158 0.132628372884672 0.224045008791891 3 | 2 0.12904361814787 0.132232461756412 0.0388576010235243 0.699866316615629 4 | 3 0.205921502989823 0.0150799800672823 0.0150799800672823 0.763918531939847 5 | 4 0.205921502989823 0.0150799800672823 0.0150799800672823 0.763918531939847 6 | 5 0.0150799800672823 0.676094740841909 0.0150799800672823 0.293745294087763 7 | 6 0.0150799800672823 0.954760054862388 0.0150799800672823 0.0150799800672823 8 | 7 0.038967474292714 0.883097580439379 0.038967474292714 0.038967474292714 9 | 8 0.132451723667602 0.132451723667602 0.132451723667602 0.602644825573624 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M205_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.13401826562045 0.13401826562045 0.515269751850903 0.216693718099645 3 | 2 0.576066202142376 0.0820013211193939 0.0820013211193939 0.25993115492169 4 | 3 0.0103561129639003 0.0103561129639003 0.0103561129639003 0.968931662045532 5 | 4 0.0103561129639003 0.0103561129639003 0.968931662045532 0.0103561129639003 6 | 5 0.0103561129639003 0.0103561129639003 0.968931662045532 0.0103561129639003 7 | 6 0.968931662045532 0.0103561129639003 0.0103561129639003 0.0103561129639003 8 | 7 0.132789784361445 0.0348932769399727 0.721998765025876 0.110318168616281 9 | 8 0.126551794603736 0.126551794603736 0.126551794603736 0.620344616885976 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M207_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.129927503815854 0.610217490054168 0.129927503815854 0.129927503815854 3 | 2 0.162169659073361 0.71524864978095 0.0612908430354122 0.0612908430354122 4 | 3 0.0985376724045964 0.198319933103713 0.015118905047773 0.688023483110874 5 | 4 0.0985376724045964 0.015118905047773 0.015118905047773 0.871224511166816 6 | 5 0.126146345272557 0.0383243064980517 0.0383243064980517 0.797205035941118 7 | 6 0.0618044057415847 0.814586783980587 0.0618044057415847 0.0618044057415847 8 | 7 0.0618044057415847 0.814586783980587 0.0618044057415847 0.0618044057415847 9 | 8 0.135300237426616 0.507774283924346 0.135300237426616 0.22162524216213 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M233_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.636978287510398 0.121007238357786 0.121007238357786 0.121007238357786 3 | 2 0.0076645345438924 0.0899452124766006 0.894725719257059 0.0076645345438924 4 | 3 0.977006397189769 0.0076645345438924 0.0076645345438924 0.0076645345438924 5 | 4 0.0076645345438924 0.612815025366319 0.0076645345438924 0.371855906367345 6 | 5 0.977006397189769 0.0076645345438924 0.0076645345438924 0.0076645345438924 7 | 6 0.0076645345438924 0.602279157965488 0.303063174624106 0.0869931336879624 8 | 7 0.977006397189769 0.0076645345438924 0.0076645345438924 0.0076645345438924 9 | 8 0.137739287624383 0.137739287624383 0.330927981049532 0.393593442517162 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M237_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.129454268482862 0.425941825198073 0.315149636864589 0.129454268482862 3 | 2 0.656153742144596 0.0844131765659118 0.0844131765659118 0.175019900014733 4 | 3 0.950383768866942 0.0165387444400462 0.0165387444400462 0.0165387444400462 5 | 4 0.0165387444400462 0.950383768866942 0.0165387444400462 0.0165387444400462 6 | 5 0.0165387444400462 0.0165387444400462 0.0165387444400462 0.950383768866942 7 | 6 0.950383768866942 0.0165387444400462 0.0165387444400462 0.0165387444400462 8 | 7 0.0637184011453699 0.808844794932511 0.0637184011453699 0.0637184011453699 9 | 8 0.305151488291231 0.137316172069145 0.336410153085593 0.221122192091636 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M071_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.203253094215648 0.126506578204249 0.543733751829296 0.126506578204249 3 | 2 0.770738546819589 0.076420483561973 0.076420483561973 0.076420483561973 4 | 3 0.00852837899556795 0.97441485920865 0.00852837899556795 0.00852837899556795 5 | 4 0.00852837899556795 0.00852837899556795 0.97441485920865 0.00852837899556795 6 | 5 0.97441485920865 0.00852837899556795 0.00852837899556795 0.00852837899556795 7 | 6 0.00852837899556795 0.97441485920865 0.00852837899556795 0.00852837899556795 8 | 7 0.152686398834125 0.0571645056272888 0.732984592797132 0.0571645056272888 9 | 8 0.340376555938508 0.132144701693306 0.395334039051656 0.132144701693306 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M085_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.12362654152578 0.12362654152578 0.629120372019251 0.12362654152578 3 | 2 0.63622367622182 0.031995773301613 0.213909974746687 0.117870572332418 4 | 3 0.492981204434788 0.302090611776618 0.00803581427420333 0.196892370229056 5 | 4 0.00803581427420333 0.00803581427420333 0.00803581427420333 0.975892557892055 6 | 5 0.00803581427420333 0.00803581427420333 0.00803581427420333 0.975892557892055 7 | 6 0.975892557892055 0.00803581427420333 0.00803581427420333 0.00803581427420333 8 | 7 0.975892557892055 0.00803581427420333 0.00803581427420333 0.00803581427420333 9 | 8 0.134900949907436 0.134900949907436 0.414188879296682 0.316009217694507 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M136_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.436277898128549 0.212217654094781 0.126891211515333 0.22461323413238 3 | 2 0.0924295127665786 0.00696502604804819 0.00696502604804819 0.893640435294675 4 | 3 0.267666430146211 0.00696502604804819 0.00696502604804819 0.71840351791504 5 | 4 0.00696502604804819 0.00696502604804819 0.979104922013202 0.00696502604804819 6 | 5 0.00696502604804819 0.979104922013202 0.00696502604804819 0.00696502604804819 7 | 6 0.979104922013202 0.00696502604804819 0.00696502604804819 0.00696502604804819 8 | 7 0.030858023739769 0.907425925530396 0.030858023739769 0.030858023739769 9 | 8 0.416799749355804 0.130114233444731 0.236904314474964 0.216181705226227 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M240_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.128696401023838 0.128696401023838 0.613910794211184 0.128696401023838 3 | 2 0.512984419562279 0.0334365356411996 0.0334365356411996 0.420142513686945 4 | 3 0.00944995452918129 0.00944995452918129 0.971650138280221 0.00944995452918129 5 | 4 0.00944995452918129 0.00944995452918129 0.00944995452918129 0.971650138280221 6 | 5 0.00944995452918129 0.00944995452918129 0.971650138280221 0.00944995452918129 7 | 6 0.101976843355563 0.00944995452918129 0.00944995452918129 0.879123249453836 8 | 7 0.125821335643637 0.0334489954414579 0.715631699697531 0.125097972332641 9 | 8 0.319373249667799 0.130770126511955 0.326057618931933 0.223799001888924 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M118_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.242299497071223 0.216883250364873 0.307446262851226 0.233370991729194 3 | 2 0.199824312378572 0.0288359153058829 0.0288359153058829 0.742503855343117 4 | 3 0.00461585480765927 0.00461585480765927 0.986152436738371 0.00461585480765927 5 | 4 0.00461585480765927 0.986152436738371 0.00461585480765927 0.00461585480765927 6 | 5 0.986152436738371 0.00461585480765927 0.00461585480765927 0.00461585480765927 7 | 6 0.00461585480765927 0.00461585480765927 0.00461585480765927 0.986152436738371 8 | 7 0.00461585480765927 0.00461585480765927 0.986152436738371 0.00461585480765927 9 | 8 0.22183301502563 0.434108746230729 0.218830778525212 0.12522746055256 10 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M325_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.42857142857143 0 0.28571428571429 0.28571428571429 3 | 2 0 0.42857142857143 0.57142857142857 0 4 | 3 0.28571428571429 0.28571428571429 0.42857142857143 0 5 | 4 0 0 0.14285714285714 0.85714285714286 6 | 5 0.14285714285714 0.28571428571429 0.28571428571429 0.28571428571429 7 | 6 0.42857142857143 0.28571428571429 0.14285714285714 0.14285714285714 8 | 7 0.28571428571429 0.28571428571429 0.42857142857143 0 9 | 8 0.14285714285714 0.57142857142857 0.14285714285714 0.14285714285714 10 | 9 0.28571428571429 0 0 0.71428571428571 11 | 10 0 0 0 1 12 | 11 0 1 0 0 13 | 12 1 0 0 0 14 | 13 0 0.71428571428571 0 0.28571428571429 15 | 14 0.28571428571429 0.57142857142857 0.14285714285714 0 16 | 15 0 1 0 0 17 | 16 0 1 0 0 18 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M328_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0.42105263157895 0.31578947368421 0.052631578947368 0.21052631578947 3 | 2 0.090909090909091 0.18181818181818 0 0.72727272727273 4 | 3 0.090909090909091 0.45454545454545 0.13636363636364 0.31818181818182 5 | 4 0.39130434782609 0.52173913043478 0.043478260869565 0.043478260869565 6 | 5 0 0 0 1 7 | 6 0.037037037037037 0 0 0.96296296296296 8 | 7 0 0 0.037037037037037 0.96296296296296 9 | 8 0.25925925925926 0.11111111111111 0.14814814814815 0.48148148148148 10 | 9 0.11111111111111 0.14814814814815 0.11111111111111 0.62962962962963 11 | 10 0.36 0.08 0.12 0.44 12 | 11 0.090909090909091 0 0.090909090909091 0.81818181818182 13 | 12 0.15 0 0.05 0.8 14 | 13 0.17647058823529 0.41176470588235 0.058823529411765 0.35294117647059 15 | 14 0.14285714285714 0.14285714285714 0.42857142857143 0.28571428571429 16 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2018 Brian Gudenas 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /Data/Motifs/pwms_all_motifs/M287_0.6.txt: -------------------------------------------------------------------------------- 1 | Pos A C G U 2 | 1 0 0 0 1 3 | 2 0 0 1 0 4 | 3 0 0 0 1 5 | 4 1 0 0 0 6 | 5 0.43478260869565 0.21739130434783 0.30434782608696 0.043478260869565 7 | 6 0.73913043478261 0 0.1304347826087 0.1304347826087 8 | 7 0.17391304347826 0.043478260869565 0 0.78260869565217 9 | 8 0.65217391304348 0 0.043478260869565 0.30434782608696 10 | 9 0.43478260869565 0.1304347826087 0.39130434782609 0.043478260869565 11 | 10 0.21739130434783 0.34782608695652 0.26086956521739 0.17391304347826 12 | 11 0.17391304347826 0.17391304347826 0.21739130434783 0.43478260869565 13 | 12 0.26086956521739 0.30434782608696 0.34782608695652 0.08695652173913 14 | 13 0.30434782608696 0.30434782608696 0.30434782608696 0.08695652173913 15 | 14 0.043478260869565 0.39130434782609 0.26086956521739 0.30434782608696 16 | 15 0 0.47826086956522 0.34782608695652 0.17391304347826 17 | 16 0.045454545454545 0.45454545454545 0.22727272727273 0.27272727272727 18 | 17 0 0.47619047619048 0.28571428571429 0.23809523809524 19 | 18 0 0.52380952380952 0.38095238095238 0.095238095238095 20 | 19 0 0.75 0.15 0.1 21 | 20 0 0.77777777777778 0.11111111111111 0.11111111111111 22 | 21 0 0.46153846153846 0.46153846153846 0.076923076923077 23 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: "README" 3 | author: "Brian Gudenas" 4 | date: "February 27, 2018" 5 | output: html_document 6 | --- 7 | 8 | ```{r setup, include=FALSE} 9 | knitr::opts_chunk$set(echo = TRUE, cache = TRUE) 10 | ``` 11 | 12 | ## DeepLncRNA 13 | 14 | DeepLncRNA is a deep learning model which predicts nuclear or cytosolic localization of lncRNAs. After cloning this repo and downloading the dependencies it can be utilized starting from either ensembl gene or transcript IDs or with a custom sequence. 15 | 16 | ## Dependencies 17 | ```{r , eval = FALSE} 18 | ## DeepLncRNA was built using h2o version h2o_3.18.0.11 19 | ## H2o models require you are running the same version therefore you will need to install the archived version 20 | install.packages("https://cran.r-project.org/src/contrib/Archive/h2o/h2o_3.18.0.11.tar.gz", repos=NULL, type="source") 21 | 22 | install.packages("dplyr") 23 | source("https://bioconductor.org/biocLite.R") 24 | biocLite(c("Biostrings","biomaRt")) 25 | ``` 26 | 27 | 28 | ```{r , message = FALSE, warning=FALSE} 29 | source("./src/DeepLncRNA.R") 30 | IDs = c("ENSG00000224294", "ENSG00000278709" ) 31 | 32 | mart = biomaRt::useMart("ensembl","hsapiens_gene_ensembl") 33 | trans = Gene2Transcript(IDs, mart) 34 | seqs = GetSeq(trans$ensembl_transcript_id, mart) 35 | df = FeatureExtract(seqs) 36 | preds = DeepLncRNA(df, df$ensembl_transcript_id) 37 | 38 | preds$gene = trans$ensembl_gene_id[match(rownames(preds), trans$ensembl_transcript_id)] 39 | preds 40 | 41 | ``` 42 | 43 | -------------------------------------------------------------------------------- /src/lnclocator_parse.R: -------------------------------------------------------------------------------- 1 | 2 | # Parse LncRNAs from LncLocator ------------------------------------------- 3 | # source("https://bioconductor.org/biocLite.R") 4 | # biocLite("seqinr") 5 | 6 | library(stringr) 7 | library(seqinr) 8 | library(Biostrings) 9 | cyto = read.fasta("./Data/LncLocator/Cytosol", as.string = TRUE) 10 | nuc = read.fasta("./Data/LncLocator/Nucleus", as.string = TRUE) 11 | seqs =c( nuc, cyto) 12 | nucnames = unlist(getAnnot(nuc)) 13 | cytonames = unlist(getAnnot(cyto)) 14 | 15 | allnames = c(nucnames, cytonames) 16 | NRs = grep( "NR_*", allnames) 17 | refseq = str_extract( allnames[NRs], "NR_\\d*") ##get Refseq IDs 18 | refseq2 = str_extract( allnames, "NM_\\d*") ##get Refseq IDs 19 | refseq2 = refseq2[!is.na(refseq2)] 20 | 21 | # mice = str_extract( allnames, "XR_\\d*") 22 | # mice = mice[!is.na(mice)] 23 | # genmice = str_extract( allnames, "AK\\d*") 24 | # genmice = genmice[!is.na(genmice)] 25 | ensem= str_extract( allnames, "ENST\\d*") ##get Ensembl IDs 26 | ensem = ensem[!is.na(ensem)] 27 | 28 | fullnames = c(refseq, refseq2, ensem) 29 | 30 | ## Get transcript biotype and chromosome if available 31 | mart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl") 32 | map = biomaRt::getBM(mart = mart, attributes = c( "gene_biotype","refseq_ncrna", "chromosome_name"), filters = "refseq_ncrna", values = refseq) 33 | mapNM = biomaRt::getBM(mart = mart, attributes = c( "gene_biotype","refseq_ncrna", "chromosome_name"), filters = "refseq_mrna", values = refseq2) 34 | map2 = biomaRt::getBM(mart = mart, attributes = c( "gene_biotype","ensembl_transcript_id" ,"chromosome_name"), filters = "ensembl_transcript_id", values = ensem) 35 | colnames(map)= c("gene_biotype","ID", "chromosome_name") 36 | colnames(mapNM)= c("gene_biotype","ID", "chromosome_name") 37 | colnames(map2)= c("gene_biotype","ID", "chromosome_name") 38 | maps = rbind(map, mapNM, map2) 39 | maps = maps[nchar(maps$chromosome_name) <3, ] 40 | maps = maps[!is.na(maps$ID), ] 41 | 42 | #Loop through to make DF 43 | fullnames = data.frame("IDs" = c(refseq, refseq2, ensem), transcript_biotype = "", chromosome_name = "",GC_content= 0, cdna = "", stringsAsFactors = FALSE) 44 | for (i in 1:nrow(fullnames)){ 45 | 46 | bio = maps$gene_biotype[maps$ID == fullnames$IDs[i]] 47 | if (length(bio) != 0 ){ 48 | fullnames$transcript_biotype[i] = bio 49 | } else {fullnames$transcript_biotype[i] = NA} 50 | 51 | chrom = maps$chromosome_name[maps$ID == fullnames$IDs[i]] 52 | if (length(chrom) != 0 ){ 53 | fullnames$chromosome[i] = chrom 54 | } else {fullnames$transcript_biotype[i] = NA} 55 | 56 | fullnames$cdna[i] = toupper(as.character(seqs[grepl(fullnames$IDs[i], allnames)])) 57 | fullnames$GC_content[i] = sum(oligonucleotideFrequency(DNAString(fullnames$cdna[i]), 1)[c(2,3)])/ sum(oligonucleotideFrequency(DNAString(fullnames$cdna[i]), 1)) 58 | } 59 | fullnames$transcript_length = as.numeric(lapply(fullnames$cdna, nchar)) 60 | fullnames = fullnames[ ,colnames(fullnames)!= "chromosome"] 61 | 62 | 63 | allseqs = data.frame("IDs" = c(allnames), transcript_biotype = "", chromosome_name = "",GC_content= 0, cdna = "", stringsAsFactors = FALSE) 64 | for (i in 1:nrow(allseqs)) { 65 | allseqs$IDs[i] = allnames[i] 66 | allseqs$cdna[i] = toupper(as.character(seqs[allseqs$IDs[i] == allnames])) 67 | allseqs$GC_content[i] = sum(oligonucleotideFrequency(DNAString(allseqs$cdna[i]), 1)[c(2,3)])/ sum(oligonucleotideFrequency(DNAString(allseqs$cdna[i]), 1)) 68 | } 69 | allseqs$transcript_length = as.numeric(lapply(allseqs$cdna, nchar)) 70 | 71 | ## FIlter out seqs from allseqs for which we got genomic features 72 | for(i in fullnames$IDs){ 73 | allseqs = allseqs[!grepl(i, allseqs$IDs), ] 74 | } 75 | 76 | master = rbind(fullnames, allseqs) 77 | 78 | master$Loc = "" 79 | for (i in 1:nrow(master)){ 80 | ID = master$IDs[i] 81 | if (sum(grepl(ID, cytonames)) == 1 ){master$Loc[i] = "Cytosol" 82 | }else if (sum(grepl(ID, nucnames)) == 1 ){master$Loc[i] = "Nuclear" 83 | }else if (sum(ID == nucnames)==1) { master$Loc[i] = "Nuclear" 84 | }else if (sum(ID == cytonames)==1) { master$Loc[i] = "Cytosol" } 85 | } 86 | 87 | 88 | source("./src/DeepLncRNA.R") 89 | lncs = FeatureExtract(master) 90 | 91 | ## Remove any lncRNAs present in training or validation data 92 | filt = is.na(match(master$IDs, c(rownames(res$train), rownames(res$validate) )) ) 93 | lncs = lncs[filt, ] 94 | preds = DeepLncRNA(lncs, lncs$IDs) 95 | 96 | caret::confusionMatrix(data = preds$predict, reference = as.factor(master$Loc[filt]), positive = "Nuclear") 97 | -------------------------------------------------------------------------------- /src/DATA_Acq.md: -------------------------------------------------------------------------------- 1 | Data Acquisition and Processing 2 | ============================= 3 | Author: Brian Gudenas 4 | 5 | Date: 4/26/2017 6 | 7 | # Description 8 | Download Data RNA-seq data from fractionated cell lines from encodeproject.org and quantify transcript abundances 9 | https://www.encodeproject.org/matrix/?type=Experiment 10 | 11 | Data from ENCODE matrix portal is obtained by using filters: 12 | 1. Homo Sapiens 13 | 2. Total RNA-seq 14 | 3. PolyA mRNA-seq 15 | 4. polyA depleted RNA-seq 16 | 5. fastq 17 | ###Copy link address from the download button and curl it below 18 | 19 | Code 20 | ====================================== 21 | #setup dirs 22 | mkdir ENCODE 23 | mkdir ENCODE/Raw ENCODE/Meta 24 | cd ENCODE/Meta 25 | 26 | ## following download link was created on 11/27/17 as described above 27 | curl https://www.encodeproject.org/batch_download/type%3DExperiment%26replicates.library.biosample.donor.organism.scientific_name%3DHomo%2Bsapiens%26assay_title%3Dtotal%2BRNA-seq%26assay_title%3DpolyA%2Bdepleted%2BRNA-seq%26assay_title%3DpolyA%2BmRNA%2BRNA-seq%26files.file_type%3Dfastq > RAW_Links.txt 28 | 29 | head -n 1 RAW_Links.txt ##metadata link in first row 30 | # may need to paste metadata link in browser if curl doesnt work 31 | curl https://www.encodeproject.org/metadata/type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&assay_title=total+RNA-seq&files.file_type=fastq/metadata.tsv > metadata.tsv 32 | ## Check total cell fractions 33 | cut -f 14 metadata.tsv | sort | uniq 34 | ##select all samples that are subcellular fractions 35 | awk 'BEGIN {FS="\t"} ($14 != "")' metadata.tsv | cut -f 42 > Subcell_DL_urls 36 | ## Download all data 37 | cd ../Raw 38 | xargs -n 1 curl -O -L < ../Meta/Subcell_DL_urls 39 | 40 | ## Create file for paired-end samples mappings contains pair1_ID, pair2_ID and read_pair number 41 | awk 'BEGIN {FS="\t"} ($14 != "")' metadata.tsv | cut -f 1,36,35 > Pair_map.txt 42 | cd .. 43 | 44 | Filter to remove duplicates 45 | ==================================== 46 | R 47 | 48 | ## Pair_map contains duplicates that need to removed (from a single sample pair 1 and pair 2 files are both rows) 49 | ## We also make sure that first file accession is always read1 and second is always read2 50 | pair = read.table("./Pair_map.txt", header = 1, fill = TRUE, stringsAsFactors = FALSE) 51 | pairing = pair 52 | pair = pair[order(pair$accession), ] 53 | 54 | new =vector(mode = "character") 55 | for ( i in 1:nrow(pair)) { 56 | pair = pair[pair$Paired != pair$File[i], ] 57 | new[i] = pair$File[i] 58 | } 59 | new = new[!is.na(new)] 60 | 61 | pairs = cbind(new, pairing$Paired[match(new, pairing$File)]) 62 | colnames(pairs) = c("Pair1","Pair2") 63 | pairs = pairs[rowSums(pairs=="")==0, ] ## remove any single-ended samples 64 | write.table(pairs, "Pair_map.txt", sep="\t", row.names =FALSE, quote=FALSE) 65 | 66 | FastQC 67 | ======================================= 68 | for i in $(ls Data ) 69 | do 70 | fastqc -t 8 Data/$i -o FastQC 71 | done 72 | 73 | Transcript Quantification - Kallisto 74 | ======================================= 75 | mkdir Kallisto 76 | cd Kallisto 77 | mkdir Annot Quant 78 | cd Annot 79 | ## Download reference fasta 80 | wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.transcripts.fa.gz 81 | 82 | ## Download ERCC Spike in file from ENCODE 83 | wget https://www.encodeproject.org/files/ENCFF001RTP/@@download/ENCFF001RTP.fasta.gz 84 | 85 | ### Build Kallisto Index on reference transcripts and ERCC spike ins 86 | kallisto index -i transcripts.idx gencode.v27.transcripts.fa.gz ENCFF001RTP.fasta.gz 87 | cd .. 88 | 89 | 90 | Transcript Quantification 91 | ======================================= 92 | INDEX=./Annot/transcripts.idx 93 | 94 | while read pair1 pair2; 95 | do 96 | 97 | kallisto quant --bias -t 16 --rf-stranded -b 50 -i $INDEX -o ./Quant/${pair1} ../Raw/${pair1}.fastq.gz ../Raw/${pair2}.fastq.gz 98 | 99 | 100 | done < ../Meta/Pair_map.txt 101 | 102 | 103 | Download RNA motifs from CISBP-RNA and MEME-suite 104 | ======================================== 105 | wget http://cisbp-rna.ccbr.utoronto.ca/tmp/Homo_sapiens_2017_07_07_1:58_pm.zip 106 | wget http://meme-suite.org/meme-software/Databases/motifs/motif_databases.12.15.tgz 107 | 108 | unzip Homo_sapiens_2017_07_07_1:58_pm.zip 109 | tar -xzvf motif_databases.12.15.tgz 110 | 111 | cp pwm_all_motifs ./Data/Raw 112 | cp /motif_databases/RNA/Ray2013_rbp_Homo_sapiens.meme ./Data/Raw 113 | 114 | 115 | -------------------------------------------------------------------------------- /src/DeepLncRNA.R: -------------------------------------------------------------------------------- 1 | # DeepLncRNA.R ------------------------------------------------------------- 2 | 3 | Gene2Transcript = function(Ensembl_gene_IDs , mart){ 4 | # Extract all transcripts for a list of ensembl gene IDs 5 | #mart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl") 6 | map = biomaRt::getBM(mart = mart, attributes = c("ensembl_gene_id", "ensembl_transcript_id","transcript_biotype"), filters = "ensembl_gene_id", values = Ensembl_gene_IDs) 7 | return(map) 8 | } 9 | 10 | 11 | GetSeq = function(Ensembl_transcript_IDs, mart, versioned=FALSE){ 12 | ## Uses transcript_Ids to extract, biotype, chromosome, cDNA sequence, transcript_length, GC % 13 | library(Biostrings) 14 | #mart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl") 15 | if(versioned == TRUE) { 16 | map = biomaRt::getBM(mart = mart, attributes = c( "ensembl_transcript_id_version","transcript_biotype", "chromosome_name"), filters = "ensembl_transcript_id_version", values = Ensembl_transcript_IDs) 17 | colnames(map)[1] <- "ensembl_transcript_id" 18 | seq = biomaRt::getSequence(id = map$ensembl_transcript_id, type="ensembl_transcript_id_version", seqType = "cdna", mart = mart) 19 | } else { 20 | map = biomaRt::getBM(mart = mart, attributes = c( "ensembl_transcript_id","transcript_biotype", "chromosome_name"), filters = "ensembl_transcript_id", values = Ensembl_transcript_IDs) 21 | seq = biomaRt::getSequence(id = map$ensembl_transcript_id, type="ensembl_transcript_id", seqType = "cdna", mart = mart) 22 | } 23 | map$cdna = seq$cdna[match(map$ensembl_transcript_id, seq$ensembl_transcript_id)] 24 | 25 | map$transcript_length = as.numeric(lapply(map$cdna, nchar)) 26 | 27 | for (i in 1:nrow(map)){ 28 | map$GC_content[i] = sum(oligonucleotideFrequency(DNAString(map$cdna[i]), 1)[c(2,3)])/ sum(oligonucleotideFrequency(DNAString(map$cdna[i]), 1)) 29 | } 30 | return(map) 31 | } 32 | 33 | 34 | Kmer_add = function(df, k){ 35 | library(Biostrings) 36 | #df must contain "cdna" column 37 | #k is largest int of k-mer 38 | kmer_mat = matrix( ncol = sum(4^seq(2, k)) , nrow = nrow(df), data =0) 39 | 40 | for (i in 1:nrow(df)){ 41 | seq =DNAString(df$cdna[i]) 42 | # len = df$transcript_length[i] 43 | index = 0 44 | for (j in 2:k) { 45 | kmers = oligonucleotideFrequency(seq, j) 46 | ind2 = index 47 | kmer_mat[i, (index + 1): (ind2 + (4^j) ) ] = as.vector(kmers) 48 | index = index + (4^j) 49 | } 50 | } 51 | 52 | nams =c() 53 | for (i in 2:k){ 54 | nams =c(nams, names(oligonucleotideFrequency(seq, i)) ) 55 | 56 | } 57 | colnames(kmer_mat) = nams 58 | df = cbind(df, kmer_mat) 59 | return(df) 60 | } 61 | 62 | 63 | RNABP_Motif_add = function(df){ 64 | library(Biostrings) 65 | 66 | motifs_dir = file.path("./Data/Motifs/pwms_all_motifs") 67 | mot_num = length(list.files(motifs_dir)) 68 | 69 | mat_mot = matrix(nrow = nrow(df), ncol = mot_num , data = 0) 70 | 71 | for (i in 1:mot_num){ 72 | fils = list.files(motifs_dir)[i] 73 | #some motif files from CISBP are empty (RFAM) and will throw an error 74 | mot = try(read.table(paste0(motifs_dir, "/", fils), sep = "\t", row.names = 1, header = TRUE ), silent = TRUE) 75 | if (class(mot) != "try-error"){ 76 | mot = t(mot) 77 | rownames(mot)[4] = "T" 78 | 79 | for (j in 1:nrow(df)){ 80 | #len = df$transcript_length[j] 81 | seq = df$cdna[j] 82 | counts = countPWM(mot, seq, min.score = "80%") 83 | mat_mot[j,i] = counts 84 | } 85 | } 86 | } 87 | 88 | df = cbind(df, mat_mot) 89 | return(df) 90 | } 91 | 92 | 93 | FeatureExtract = function(map){ 94 | library(dplyr) 95 | ## Use cDNA sequence to compute kmer frequencies and RNA binding motifs 96 | df = Kmer_add(map, k = 5) 97 | df = RNABP_Motif_add(df) 98 | ######################### 99 | # Add biotype and chromosome feature 100 | df$lincRNA = 0 101 | df$lincRNA[df$transcript_biotype == "lincRNA"] = 1 102 | 103 | df$antisense = 0 104 | df$antisense[df$transcript_biotype == "antisense"] = 1 105 | 106 | df$sense = 0 107 | df$sense[grepl("^sense_", df$transcript_biotype)] = 1 108 | 109 | df = df %>% dplyr::select(-transcript_biotype) 110 | df$chromosome_name = as.factor(df$chromosome_name) 111 | 112 | chroms = data.frame(matrix(nrow=nrow(df), ncol = 24, data = 0)) 113 | colnames(chroms) = paste0("chromosome_name", c(1:22, "X","Y")) 114 | for ( i in 1:nrow(df)){ 115 | chroms[i, colnames(chroms) == paste0("chromosome_name", df$chromosome_name[i]) ] = 1 116 | } 117 | 118 | 119 | df = cbind(df, chroms) 120 | df = df %>% dplyr::select( - chromosome_name) 121 | 122 | return(df) 123 | } 124 | 125 | 126 | DeepLncRNA = function(df, IDs){ 127 | library(h2o) 128 | localH2O = h2o.init(ip="localhost", port = 54321, startH2O = TRUE, nthreads = 1, max_mem_size = "1G") 129 | DNN = h2o.loadModel("./Data/Models/DeepLncRNA") 130 | pred_hex = as.h2o(df) 131 | vals = as.data.frame(predict(DNN, pred_hex, "probs")) 132 | rownames(vals) = IDs 133 | h2o.shutdown(FALSE) 134 | return(vals) 135 | } 136 | 137 | ##Usage example 138 | # #Usage 139 | # trans = Gene2Transcript(c("ENSG00000229807", "ENSG00000228630")) 140 | # lncRNAs = GetSeq(trans$ensembl_transcript_id) 141 | # df = FeatureExtract(lncRNAs) 142 | # preds = DeepLncRNA(df) 143 | 144 | -------------------------------------------------------------------------------- /src/LncRNA_subcell.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: Prediction of LncRNA Subcellular Localization with Deep Learning from Sequence Features 3 | author: "Brian Gudenas" 4 | date: "February 16, 2018" 5 | output: word_document 6 | --- 7 | # Prediction of LncRNA Subcellular Localization with Deep Learning from Sequence Features 8 | 9 | 10 | ```{r setup, include=FALSE} 11 | library(knitr) 12 | knitr::opts_chunk$set(echo = TRUE, message = FALSE, cache = TRUE) 13 | opts_knit$set(root.dir = "..") 14 | ``` 15 | 16 | ```{r Libraries, warning = FALSE} 17 | library(readr) 18 | library(stringr) 19 | library(sleuth) 20 | library(dplyr) 21 | library(RUVSeq) 22 | library(RColorBrewer) 23 | library(pheatmap) 24 | ``` 25 | 26 | ## Load Sample Metadata 27 | 28 | ```{r metadata, warning = FALSE} 29 | samples = read_tsv("./Data/Meta/metadata.tsv") 30 | colnames(samples) = make.names(colnames(samples)) 31 | Pair = read.table("./Data/Meta/Pair_map.txt", sep="\t", header = TRUE) 32 | 33 | samples = samples[!is.na(match(samples$File.accession, Pair$Pair1)), ] 34 | 35 | samples = samples[samples$Biosample.subcellular.fraction.term.name == "nucleus" | samples$Biosample.subcellular.fraction.term.name == "cytosol", ] 36 | 37 | samples$Library.depleted.in[is.na(samples$Library.depleted.in)] = "rRNA" 38 | samples$Lib_method = paste0(samples$Library.made.from,"_", samples$Library.depleted.in) 39 | 40 | s2c = dplyr::select(samples, sample = File.accession, condition = Biosample.subcellular.fraction.term.name, cell = Biosample.term.name, platform = Platform, Lib = Lib_method, reads = Read.length, warning = Audit.WARNING) 41 | 42 | ## Remove any cell types with less than 4 total samples 43 | s2c = s2c[is.na(match(s2c$cell, names(table(s2c$cell))[table(s2c$cell) < 4] ) ), ] 44 | 45 | filespath = file.path(getwd(), "/Data/Kallisto/Quant", s2c$sample) 46 | s2c = dplyr::mutate(s2c, path = filespath) 47 | 48 | ## Total samples 49 | nrow(s2c) 50 | ## Samples per fraction 51 | table(s2c$condition) 52 | ## Samples per Library type 53 | table(s2c$Lib) 54 | ## Cell types 55 | table(s2c$cell) 56 | 57 | ## Kallisto.o* is the standard output from the kallisto quant call for all samples 58 | output = read.delim(file = "./Data/Kallisto/Kallisto.o2139569", sep = "\n") 59 | pairmap = read.delim(file ="./Data/Meta/Pair_map.txt") 60 | 61 | alignments = output[grepl("processed", output[,1]), ] 62 | 63 | pairmap$total_reads = as.numeric(str_trim(str_replace_all(unlist(lapply(str_split(unlist(lapply(str_split(unlist(lapply(str_split(alignments, ", "), "[[", 1)), " reads"), "[[", 1)), "processed"),"[[",2)),",",""))) 64 | pairmap$reads_aligned = as.numeric(str_replace_all(unlist(lapply(str_split(unlist(lapply(str_split(alignments, ", "), "[[", 2)), " reads"), "[[", 1)), ",","")) 65 | 66 | pairmap$percent_aligned = pairmap$reads_aligned/pairmap$total_reads*100 67 | s2c$total_reads = pairmap$total_reads[match(s2c$sample, pairmap$Pair1)] 68 | s2c$reads_aligned = pairmap$reads_aligned[match(s2c$sample, pairmap$Pair1)] 69 | 70 | ## total aligned reads 71 | sum(s2c$reads_aligned) 72 | 73 | rm(alignments, samples, pairmap, Pair, output) 74 | write.csv(s2c, "./Data/Meta/Sample_Meta.csv") 75 | ``` 76 | 77 | ## DTE by cell type 78 | Perform differential transcript expression analysis for each cell type. If a cell type contains more than a single RNA library construction protocol then we utilize library type as a covariate in the DTE test. 79 | 80 | 81 | ```{r DTE_loop, warning = FALSE} 82 | master =c() 83 | for ( i in unique(s2c$cell)){ 84 | s2c_tmp = dplyr::filter(s2c, cell == i) %>% arrange(sample) 85 | 86 | so = sleuth_prep(s2c_tmp, transformation_function = function(x) log2(x+0.5), extra_bootstrap_summary = TRUE) 87 | lds = plot_pc_variance(so) 88 | 89 | plot_pca(so, color_by = "condition", text_labels = TRUE) + xlab(paste("PC1","%Var =", round(lds$data[1,2],2))) + ylab(paste("PC2","Var =", round(lds$data[2,2],2))) 90 | 91 | ## if more than 1 RNA-seq library protocols were used account for Lib covariate 92 | if (length(unique(s2c_tmp$Lib)) > 1 ) { 93 | 94 | so <- sleuth_fit(so, ~ Lib + condition, 'full') 95 | so <- sleuth_fit(so, ~ Lib, 'reduced') 96 | so = sleuth_wt(so, "conditionnucleus") 97 | wt_results = sleuth_results(so, 'conditionnucleus') 98 | res =wt_results[!is.na(wt_results$pval), ] 99 | res$target_id = unlist(lapply(str_split(res$target_id, "\\."), "[[", 1)) 100 | out_name = paste0("./Data/tables/DTE","_",i, ".tsv") 101 | write.table(res, out_name, sep = "\t", quote = FALSE, row.names = FALSE) 102 | res$cell = i 103 | 104 | master = rbind(master,res) 105 | 106 | } else { 107 | 108 | Expr = so$obs_norm %>% dplyr::select(target_id, sample, est_counts) 109 | Emat = tidyr::spread(Expr, key = sample, est_counts) 110 | rownames(Emat) = unlist(lapply(str_split(Emat[,1],"\\|"), "[[",1)) 111 | Emat = as.matrix(Emat[,-1]) 112 | #dim(Emat) 113 | ## need to round est_counts to integer for RUVseq 114 | Emat = round(Emat) 115 | 116 | # Filter transcripts 117 | filter <- apply(Emat, 1, function(x) length(x[x > 5]) >= 2) ##remove non-expressed transcripts (5 counts in 2 samples) 118 | filtered <- Emat[filter,] 119 | EDASeq::plotPCA(filtered, col=as.numeric(as.factor(s2c_tmp$condition))+2, cex=1.2, k=3, pch = as.numeric(as.factor(s2c_tmp$Lib)), main = paste("Sleuth",i) ) 120 | 121 | so <- sleuth_fit(so, ~ condition, 'full') 122 | so <- sleuth_fit(so, ~ 1, 'reduced') 123 | so <- sleuth_lrt(so, 'reduced', 'full') 124 | so = sleuth_wt(so, "conditionnucleus") 125 | wt_results = sleuth_results(so, 'conditionnucleus') 126 | res =wt_results[!is.na(wt_results$pval), ] 127 | res$target_id = unlist(lapply(str_split(res$target_id, "\\."), "[[", 1)) 128 | out_name = paste0("./Data/tables/DTE","_",i, ".tsv") 129 | write.table(res, out_name, sep = "\t", quote = FALSE, row.names = FALSE) 130 | res$cell = i 131 | 132 | master = rbind(master,res) 133 | } 134 | 135 | } 136 | 137 | write.csv(master, "./Data/tables/Master.csv", quote = FALSE, row.names = FALSE) 138 | rm(Emat,Expr,filtered,Pair,pairmap, res, samples, wt_results, alignments, filter, set,set1,so, output, s2c_tmp, filespath, i, out_name, wts,x) 139 | ``` 140 | 141 | ## LncRNA Filter 142 | 143 | ```{r, lncRNA_preprocess} 144 | master = read.csv("./Data/tables/Master.csv", header = TRUE, stringsAsFactors = FALSE) 145 | 146 | annots = rtracklayer::readGFF(gzfile("./Data/Annotation/gencode.v28.long_noncoding_RNAs.gtf.gz"), version = 2L) 147 | annots = dplyr::filter(annots, type == "transcript") 148 | # remove trailing decimal 149 | annots$transcript_id = lapply(strsplit(annots$transcript_id, "\\."), "[[", 1) 150 | 151 | lnc_match = match(master$target_id, annots$transcript_id) 152 | 153 | lncRNAs = master[!is.na(lnc_match), ] 154 | 155 | ## set up Expression matrix lncRNAs x cell_type 156 | mat = matrix(nrow = length(unique(lncRNAs$target_id)), ncol = length(unique(lncRNAs$cell)), data = NA) 157 | colnames(mat) = unique(lncRNAs$cell) 158 | rownames(mat) = unique(lncRNAs$target_id) 159 | 160 | ## Loop through and add fold-changes, leave NA if not detected 161 | for (i in 1:nrow(lncRNAs)){ 162 | l2fc = lncRNAs$b[i] 163 | target = lncRNAs$target_id[i] 164 | celltype = lncRNAs$cell[i] 165 | 166 | mat[rownames(mat) == target, colnames(mat) == celltype] = l2fc 167 | } 168 | 169 | wts = table(s2c$cell)/nrow(s2c) 170 | wts = wts[order(names(wts)) ] 171 | 172 | mat = mat[ , order(colnames(mat))] 173 | 174 | df = data.frame(target_id = rownames(mat)) 175 | df$l2fc = NA 176 | 177 | for (i in 1:nrow(mat)){ 178 | 179 | df$l2fc[i] = weighted.mean(mat[i,], wts, na.rm = TRUE) 180 | } 181 | 182 | ``` 183 | ```{r, Feature_Functions} 184 | # DeepLncRNA.R ------------------------------------------------------------- 185 | 186 | Gene2Transcript = function(Ensembl_gene_IDs , mart ){ 187 | # Extract all transcripts for a list of ensembl gene IDs 188 | #mart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl") 189 | map = biomaRt::getBM(mart = mart, attributes = c("ensembl_gene_id", "ensembl_transcript_id","transcript_biotype"), filters = "ensembl_gene_id", values = Ensembl_gene_IDs) 190 | return(map) 191 | } 192 | 193 | 194 | GetSeq = function(Ensembl_transcript_IDs, mart){ 195 | ## Uses transcript_Ids to extract, biotype, chromosome, cDNA sequence, transcript_length, GC % 196 | library(Biostrings) 197 | #mart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl") 198 | map = biomaRt::getBM(mart = mart, attributes = c( "ensembl_transcript_id","transcript_biotype", "chromosome_name"), filters = "ensembl_transcript_id", values = Ensembl_transcript_IDs) 199 | seq = biomaRt::getSequence(id = map$ensembl_transcript_id, type="ensembl_transcript_id", seqType = "cdna", mart = mart) 200 | map$cdna = seq$cdna[match(map$ensembl_transcript_id, seq$ensembl_transcript_id)] 201 | 202 | map$transcript_length = as.numeric(lapply(map$cdna, nchar)) 203 | 204 | for (i in 1:nrow(map)){ 205 | map$GC_content[i] = sum(oligonucleotideFrequency(DNAString(map$cdna[i]), 1)[c(2,3)])/ sum(oligonucleotideFrequency(DNAString(map$cdna[i]), 1)) 206 | } 207 | return(map) 208 | } 209 | 210 | 211 | Kmer_add = function(df, k){ 212 | library(Biostrings) 213 | #df must contain "cdna" column 214 | #k is largest int of k-mer 215 | kmer_mat = matrix( ncol = sum(4^seq(2, k)) , nrow = nrow(df), data =0) 216 | 217 | for (i in 1:nrow(df)){ 218 | seq =DNAString(df$cdna[i]) 219 | # len = df$transcript_length[i] 220 | index = 0 221 | for (j in 2:k) { 222 | kmers = oligonucleotideFrequency(seq, j) 223 | ind2 = index 224 | kmer_mat[i, (index + 1): (ind2 + (4^j) ) ] = as.vector(kmers) 225 | index = index + (4^j) 226 | } 227 | } 228 | 229 | nams =c() 230 | for (i in 2:k){ 231 | nams =c(nams, names(oligonucleotideFrequency(seq, i)) ) 232 | 233 | } 234 | colnames(kmer_mat) = nams 235 | df = cbind(df, kmer_mat) 236 | return(df) 237 | } 238 | 239 | 240 | RNABP_Motif_add = function(df){ 241 | library(Biostrings) 242 | 243 | motifs_dir = file.path("./Data/Motifs/pwms_all_motifs") 244 | mot_num = length(list.files(motifs_dir)) 245 | 246 | mat_mot = matrix(nrow = nrow(df), ncol = mot_num , data = 0) 247 | 248 | for (i in 1:mot_num){ 249 | fils = list.files(motifs_dir)[i] 250 | #some motif files from CISBP are empty (RFAM) and will throw an error 251 | mot = try(read.table(paste0(motifs_dir, "/", fils), sep = "\t", row.names = 1, header = TRUE ), silent = TRUE) 252 | if (class(mot) != "try-error"){ 253 | mot = t(mot) 254 | rownames(mot)[4] = "T" 255 | 256 | for (j in 1:nrow(df)){ 257 | #len = df$transcript_length[j] 258 | seq = df$cdna[j] 259 | counts = countPWM(mot, seq, min.score = "80%") 260 | mat_mot[j,i] = counts 261 | } 262 | } 263 | } 264 | 265 | df = cbind(df, mat_mot) 266 | return(df) 267 | } 268 | 269 | 270 | FeatureExtract = function(map){ 271 | library(dplyr) 272 | ## Use cDNA sequence to compute kmer frequencies and RNA binding motifs 273 | df = Kmer_add(map, k = 5) 274 | df = RNABP_Motif_add(df) 275 | ######################### 276 | # Add biotype and chromosome feature 277 | df$lincRNA = 0 278 | df$lincRNA[df$transcript_biotype == "lincRNA"] = 1 279 | 280 | df$antisense = 0 281 | df$antisense[df$transcript_biotype == "antisense"] = 1 282 | 283 | df$sense = 0 284 | df$sense[grepl("^sense_", df$transcript_biotype)] = 1 285 | 286 | df = df %>% dplyr::select(-transcript_biotype) 287 | df$chromosome_name = as.factor(df$chromosome_name) 288 | 289 | chroms = data.frame(matrix(nrow=nrow(df), ncol = 24, data = 0)) 290 | colnames(chroms) = paste0("chromosome_name", c(1:22, "X","Y")) 291 | for ( i in 1:nrow(df)){ 292 | chroms[i, colnames(chroms) == paste0("chromosome_name", df$chromosome_name[i]) ] = 1 293 | } 294 | 295 | 296 | df = cbind(df, chroms) 297 | df = df %>% dplyr::select( - chromosome_name) 298 | 299 | return(df) 300 | } 301 | 302 | 303 | DeepLncRNA = function(df, IDs){ 304 | library(h2o) 305 | localH2O = h2o.init(ip="localhost", port = 54321, startH2O = TRUE, nthreads = 1, max_mem_size = "1G") 306 | DNN = h2o.loadModel("./Data/Models/DeepLncRNA") 307 | pred_hex = as.h2o(df) 308 | vals = as.data.frame(predict(DNN, pred_hex, "probs")) 309 | rownames(vals) = IDs 310 | h2o.shutdown(FALSE) 311 | return(vals) 312 | } 313 | 314 | ##Usage example 315 | # #Usage 316 | # trans = Gene2Transcript(c("ENSG00000229807", "ENSG00000228630")) 317 | # lncRNAs = GetSeq(trans$ensembl_transcript_id) 318 | # df = FeatureExtract(lncRNAs) 319 | # preds = DeepLocal(df) 320 | 321 | 322 | 323 | ``` 324 | 325 | ## Feature Extraction 326 | 327 | ```{r, feature_extraction} 328 | #source("./src/DeepLncRNA.R") 329 | mart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl") 330 | trans = GetSeq(df$target_id, mart) 331 | trans = cbind(df$l2fc[match(trans$ensembl_transcript_id, df$target_id)], trans) 332 | colnames(trans)[1] = "l2fc" 333 | df = FeatureExtract(trans) 334 | 335 | ``` 336 | 337 | ## Histogram of LncRNA localization and class selection 338 | ```{r, localization_histogram} 339 | quantile(df$l2fc) 340 | ## Select top quantile as positive set and bottom quantile as negative set 341 | ## Round to nice numbers (Cytosolic = < 0, Nuclear >= 2.8) 342 | # Make Histogram of L2FC dist 343 | h = hist(df$l2fc ) 344 | cuts <- cut(h$breaks, c(-Inf,-1,2.8,Inf)) 345 | 346 | plot(h, col = c("blue","white","red")[cuts], xlim = range(-7, 7), xlab = expression("Log"[2]* " Fold-Change"), main = "", cex.lab = 1.2) 347 | 348 | cyto = sum(df$l2fc < 0) 349 | nuc = sum(df$l2fc > 2.8) 350 | 351 | text(paste(cyto, "Cytosolic"), x = -2, y = 2200, col = "blue", cex = 1.3) 352 | text(paste(nuc, "Nuclear"), x = 5.8, y = 2200, col = "red", cex = 1.3) 353 | 354 | ``` 355 | 356 | 357 | ## Create training dataset 358 | 359 | ```{r partition_frames} 360 | rownames(df) = df$ensembl_transcript_id 361 | df = df %>% dplyr::select( -c(cdna, ensembl_transcript_id)) 362 | 363 | drop_vars = colnames(df[ ,4:ncol(df)])[colSums(df[ ,4:ncol(df)])==0] 364 | df = df %>% dplyr::select( -one_of(drop_vars)) 365 | saveRDS(df, "./Data/feature_set.rds") 366 | 367 | df = df[df$l2fc < 0 | df$l2fc > 2.8, ] 368 | df$Loc = "Nuclear" 369 | df$Loc[df$l2fc < 0] = "Cytosol" 370 | df$Loc = as.factor(df$Loc) 371 | dim(df) 372 | table(df$Loc) 373 | write.csv(df, "./Data/LncRNA_dataset.csv") 374 | 375 | set.seed(4321) 376 | spec = c(train = .7, test = .15, validate = .15) 377 | 378 | g = sample(cut( 379 | seq(nrow(df)), 380 | nrow(df)*cumsum(c(0,spec)), 381 | labels = names(spec) 382 | )) 383 | 384 | res = split(df, g) 385 | 386 | lapply(res, dim) 387 | #Check splits dont contain duplicates == FALSE 388 | table(duplicated(c(rownames(res$train), rownames(res$test), rownames(res$validate)))) 389 | 390 | # Save final dataframes 391 | saveRDS(res, "./Data/Training_frames.rds") 392 | ``` 393 | 394 | ## Deep Learning 395 | 396 | ```{r, DNN, eval = FALSE} 397 | ##Run on cluster 398 | res = readRDS("./Data/Training_frames.rds") 399 | library(h2o) 400 | localH2O = h2o.init(ip="localhost", port = 54321, startH2O = TRUE, nthreads = 24, max_mem_size = "48G") 401 | train_hex = as.h2o(res$train[ ,-1]) 402 | valid_hex = as.h2o(res$validate[ ,-1]) 403 | test_hex = as.h2o(res$validate[ ,-1]) 404 | 405 | hyper_params <- list( 406 | activation=c("RectifierWithDropout"), 407 | hidden =list( c(500,250,125), c(256, 128,64) c(128,64,32), c(64,32,16), c(32,16,8) ), 408 | input_dropout_ratio=c(0, 0.1, 0.2, 0.3, 0.4), 409 | l1 = c(1e-5, 1e-4, 1e-3, 0), 410 | l2 = c(1e-5, 1e-4, 1e-3, 0) 411 | ) 412 | 413 | search_criteria = list(strategy = "RandomDiscrete", max_models = 800, seed=54321, stopping_rounds=5, stopping_tolerance=1e-3) 414 | 415 | dl_random_grid <- h2o.grid( 416 | algorithm="deeplearning", 417 | grid_id = "dl_grid", 418 | training_frame=train_hex, 419 | validation_frame = valid_hex, 420 | x=1:1582, 421 | y=1583, 422 | epochs= 400, 423 | stopping_metric="misclassification", 424 | stopping_tolerance=1e-2, 425 | stopping_rounds=5, 426 | hyper_params = hyper_params, 427 | search_criteria = search_criteria 428 | ) 429 | 430 | grid <- h2o.getGrid("dl_grid",sort_by="accuracy", decreasing=TRUE) 431 | 432 | best_model <- h2o.getModel(grid@model_ids[[1]]) 433 | best_model 434 | 435 | h2o.saveModel(best_model, path="./Data/Models/", force=TRUE) 436 | file.rename(paste0("./Data/Models/", best_model@model_id), "./Data/Models/DeepLncRNA") 437 | h2o.shutdown(FALSE) 438 | 439 | ``` 440 | 441 | ##Create Models for comparison 442 | 443 | ```{r, model_building, eval = FALSE} 444 | library(randomForest) 445 | library(doParallel) 446 | library(caret) 447 | 448 | 449 | res = readRDS("./Data/Training_frames.rds") 450 | cluster <- makeCluster(detectCores()) 451 | registerDoParallel(cluster) 452 | 453 | logit <- caret::train(Loc ~., 454 | data = res$train[ ,-1], 455 | method = "LogitBoost", 456 | preProcess = c("center", "scale"), 457 | trControl = trainControl(classProbs = TRUE), 458 | allowParralel = TRUE, 459 | tuneLength = 6) 460 | 461 | gbm <- caret::train(Loc ~., 462 | data = res$train[ ,-1], 463 | method = "gbm", 464 | preProcess = c("center", "scale"), 465 | trControl = trainControl(classProbs = TRUE), 466 | allowParralel = TRUE, 467 | tuneLength = 6) 468 | 469 | svm_radial <- caret::train(Loc ~., 470 | data = res$train[ ,-1], 471 | method = "svmRadial", 472 | preProcess = c("center", "scale"), 473 | trControl = trainControl(classProbs = TRUE), 474 | allowParralel = TRUE, 475 | tuneLength = 6) 476 | 477 | rf <- caret::train(Loc ~ ., data = res$train[ ,-1], method = "rf", 478 | allowParralel = TRUE, 479 | tuneLength = 6, 480 | ntree = 101) 481 | 482 | stopCluster(cluster) 483 | registerDoSEQ() 484 | 485 | saveRDS(gbm, "./Data/Models/gbm.rds") 486 | saveRDS(logit, "./Data/Models/Logit.rds") 487 | saveRDS(svm_radial, "./Data/Models/SVM.rds") 488 | saveRDS(rf, "./Data/Models/RF.rds") 489 | ``` 490 | 491 | 492 | 493 | ```{r, Feature_evaluation} 494 | DNN 495 | 496 | feats = DNN@model$variable_importances 497 | 498 | map = match( feats$variable, colnames(df)) 499 | feats$index = map 500 | feats = feats[order(feats$index), ] 501 | 502 | ## Find indexs of feature sets 503 | ## subtract one since we are removing L2FC 504 | kmers = c(4:1363)-1 505 | RBPs = c(1364:1556)-1 506 | genomic = c(2,3,1557:1583)-1 507 | 508 | ## Check for all features 509 | length(c(kmers,RBPs,genomic)) == nrow(feats) 510 | 511 | ksum = sum(feats$relative_importance[kmers])/length(kmers) 512 | rsum = sum(feats$relative_importance[RBPs])/length(RBPs) 513 | gsum = sum(feats$relative_importance[genomic])/length(genomic) 514 | 515 | feats = feats[order(feats$relative_importance, decreasing = TRUE), ] 516 | feats[1,6] = ksum 517 | feats[1,7] = rsum 518 | feats[1,8] = gsum 519 | colnames(feats)[6:8] = c("Normalized_Kmer_Sum", "Normalized_RBP_Sum", "Normalized_Genomic_Sum") 520 | 521 | feats[1,9] = sum(feats$percentage[kmers])*100 522 | feats[1,10] = sum(feats$percentage[RBPs])*100 523 | feats[1,11] = sum(feats$percentage[genomic])*100 524 | colnames(feats)[9:11] = c("Percent_Kmer_Sum", "Percent_RBP_Sum", "Percent_Genomic_Sum") 525 | write.csv(feats, "./Data/feature_importance.csv") 526 | ``` 527 | 528 | ## Machine learning model comparison on validation set 529 | 530 | ```{r, model_comparison, fig.height= 7, fig.width= 5} 531 | library(h2o) 532 | library(caret) 533 | logit = readRDS("./Data/Models/Logit.rds") 534 | gbm = readRDS("./Data/Models/gbm.rds") 535 | rf = readRDS("./Data/Models/RF.rds") 536 | SVM = readRDS("./Data/Models/SVM.rds") 537 | 538 | localH2O = h2o.init(ip="localhost", port = 54321, startH2O = TRUE, nthreads = 1, max_mem_size = "2G") 539 | DNN = h2o.loadModel("./Data/Models/DeepLncRNA") 540 | 541 | 542 | train_hex = as.h2o(res$train) 543 | valid_hex = as.h2o(res$validate) 544 | test_hex = as.h2o(res$test) 545 | 546 | 547 | ## Make plot of validation accuracies 548 | log_vals = predict(logit, res$validate) 549 | log_conf = confusionMatrix(log_vals, res$validate$Loc, positive = "Nuclear") 550 | 551 | gbm_vals = predict(gbm, res$validate) 552 | gbm_conf = confusionMatrix(gbm_vals, res$validate$Loc, positive = "Nuclear") 553 | 554 | rf_vals = predict(rf, res$validate) 555 | rf_conf = confusionMatrix(rf_vals, res$validate$Loc, positive = "Nuclear") 556 | 557 | svm_vals = predict(SVM, res$validate) 558 | svm_conf = confusionMatrix(svm_vals, res$validate$Loc, positive = "Nuclear") 559 | 560 | DNN_conf = h2o.confusionMatrix(DNN@model$validation_metrics) 561 | DNN_conf$overall = (DNN_conf[1,1]+DNN_conf[2,2])/1302 562 | 563 | 564 | 565 | GetMets = function(confMat){ 566 | ## get acc, sens, spec, F1 from caret confusion matrix 567 | acc = confMat$overall[1] 568 | spec = confMat$table[1,1]/(confMat$table[1,1] + confMat$table[2,1]) 569 | sens = confMat$table[2,2]/(confMat$table[2,2] + confMat$table[1,2]) 570 | prec = confMat$table[2,2]/(confMat$table[2,2] + confMat$table[2,1]) 571 | F1 = (2*prec*sens )/ (prec+sens) 572 | mets = c(acc,sens,spec,F1) 573 | names(mets) = c("Accuracy","Sensitivity","Specificity","F1") 574 | return(mets) 575 | } 576 | 577 | 578 | h2oGetMets = function(confMat){ 579 | ##h2o confmat has axis flipped 580 | acc = (DNN_conf[1,1]+DNN_conf[2,2])/1302 581 | spec = confMat[1,1]/(confMat[1,1] + confMat[1,2]) 582 | sens = confMat[2,2]/(confMat[2,2] + confMat[2,1]) 583 | 584 | reca = confMat[2,2]/(confMat[2,2] + confMat[1,2]) 585 | prec = confMat[2,2]/(confMat[2,2] + confMat[2,1]) 586 | F1 = (2*prec*reca )/ (prec+reca) 587 | mets = c(acc,sens,spec,F1) 588 | names(mets) = c("Accuracy","Sensitivity","Specificity","F1") 589 | return(mets) 590 | } 591 | 592 | valid_mets = data.frame( Log = GetMets(log_conf),GBM = GetMets(gbm_conf), RF = GetMets(rf_conf), SVM = GetMets(svm_conf), DeepLncRNA = h2oGetMets(DNN_conf), Metrics = names(GetMets(rf_conf))) %>% 593 | tidyr::gather(valid_mets, Metrics) 594 | valid_mets$Metric = rep(c("Accuracy","Sensitivity","Specificity","F1"), 5) 595 | colnames(valid_mets) = c("Model","Value", "Metric") 596 | 597 | ggplot(data = valid_mets, aes(as.factor(Model), Value, fill = Metric) ) + 598 | geom_bar( stat = "identity", position = "dodge") + 599 | scale_fill_brewer(palette = "Dark2") + 600 | coord_cartesian(ylim=c(0.5,.85)) + 601 | xlab("Model") + 602 | theme_bw() + 603 | theme(axis.text=element_text(size=14), 604 | axis.title=element_text(size=14,face="bold"), legend.title = element_text(size=14,face="bold")) + 605 | theme(legend.text=element_text(size=14)) 606 | ggsave("./Figures/Model_Comparison.pdf") 607 | 608 | dnn_test = as.data.frame(predict(DNN, test_hex)) 609 | rf_test = predict(rf, res$test, "prob") 610 | svm_test = predict(SVM, res$test, "prob") 611 | gbm_test = predict(gbm, res$test, "prob") 612 | logit_test = predict(logit, res$test, "prob") 613 | 614 | ``` 615 | 616 | 617 | ## Model evalutation on test set 618 | 619 | ```{r, ROC, fig.height= 6, fig.width= 6} 620 | 621 | gbm_roc =pROC::roc(predictor=as.vector(gbm_test$Nuclear), 622 | response=res$test$Loc, 623 | levels=levels(res$test$Loc) ) 624 | 625 | logit_roc =pROC::roc(predictor=as.vector(logit_test$Nuclear), 626 | response=res$test$Loc, 627 | levels=levels(res$test$Loc) ) 628 | 629 | dnn_roc = pROC::roc(predictor=as.vector(dnn_test$Nuclear), 630 | response=res$test$Loc, 631 | levels=levels(res$test$Loc) ) 632 | 633 | pdf("./Figures/AUROC.pdf") 634 | plot(dnn_roc, col = "blue", cex.lab = 1.3, cex.axis = 1, lwd=3) 635 | 636 | rf_roc =pROC::roc(predictor=as.vector(rf_test$Nuclear), 637 | response=res$test$Loc, 638 | levels=levels(res$test$Loc) ) 639 | 640 | plot(rf_roc, add = TRUE, col = "darkorange",lty=2, lwd = 3) 641 | 642 | svm_roc = pROC::roc(predictor=as.vector(svm_test$Nuclear), 643 | response=res$test$Loc, 644 | levels=levels(res$test$Loc) ) 645 | plot(svm_roc, add = TRUE, col = "magenta",lty =3, lwd = 3) 646 | 647 | plot(logit_roc, add = TRUE, col = "red",lty=4, lwd = 3) 648 | plot(gbm_roc, add = TRUE, col = "darkgreen",lty=5, lwd = 3) 649 | 650 | 651 | legend(0.35, 0.35, legend=c("DNN", "RF", "SVM","Log","GBM", "Random Guess"), 652 | col=c("blue", "darkorange","magenta","red","green","grey"), lty = c(1, 2,3,4,5,1), lwd = c(3,3,3,2,2,2), cex = 1.2) 653 | dev.off() 654 | ``` 655 | 656 | ## Test set performance metrics 657 | 658 | ```{r, testset_metrics} 659 | rf_test = predict(rf, res$test) 660 | svm_test = predict(SVM, res$test) 661 | gbm_test = predict(gbm, res$test) 662 | logit_test = predict(logit, res$test) 663 | 664 | 665 | gbm_conf = confusionMatrix(gbm_test, res$test$Loc, positive = "Nuclear") 666 | logit_conf = confusionMatrix(logit_test, res$test$Loc, positive = "Nuclear") 667 | rf_conf = confusionMatrix(rf_test, res$test$Loc, positive = "Nuclear") 668 | svm_conf = confusionMatrix(svm_test, res$test$Loc, positive = "Nuclear") 669 | 670 | DNN_conf = h2o.confusionMatrix(h2o.performance(DNN, test_hex)) 671 | DNN_conf$overall = (DNN_conf[1,1]+DNN_conf[2,2])/nrow(res$test) 672 | 673 | test_mets = data.frame(t(data.frame(GBM = GetMets(gbm_conf), Log = GetMets(log_conf), RF = GetMets(rf_conf), SVM = GetMets(svm_conf), DNN = h2oGetMets(DNN_conf)) )) 674 | test_mets$AUC = c( gbm_roc$auc, logit_roc$auc, rf_roc$auc, svm_roc$auc, dnn_roc$auc) 675 | 676 | gbm_mcc = mltools::mcc(preds = as.numeric(gbm_test)-1, actuals = as.numeric(res$test$Loc)-1) 677 | logit_mcc = mltools::mcc(preds = as.numeric(logit_test)-1, actuals = as.numeric(res$test$Loc)-1) 678 | rf_mcc = mltools::mcc(preds = as.numeric(rf_test)-1, actuals = as.numeric(res$test$Loc)-1) 679 | svm_mcc = mltools::mcc(preds = as.numeric(svm_test)-1, actuals = as.numeric(res$test$Loc)-1) 680 | dnn_mcc = mltools::mcc(preds = as.numeric(as.factor(as.vector(dnn_test$predict)))-1, actuals = as.numeric(res$test$Loc)-1) 681 | 682 | test_mets$MCC = c(gbm_mcc, logit_mcc, rf_mcc, svm_mcc, dnn_mcc) 683 | write.csv(round(test_mets, 3), "./Data/test_metrics.csv") 684 | 685 | ``` 686 | 687 | 688 | ## Differentially localized lncRNA heatmap 689 | 690 | ```{r, lncRNA_heatmap, fig.height= 7, fig.width= 5} 691 | mat_match = match(rownames(mat), rownames(df)) 692 | mat = mat[!is.na(mat_match), ] 693 | 694 | div_cols = unlist(list(color = brewer.pal(11, "RdYlBu")))[11:1] 695 | mat2 = mat 696 | mat2[mat2 >= 7] = 7 697 | mat2[mat2 <= -5] = -5 698 | mat_breaks = c(min(mat2, na.rm = TRUE), -3, -1, 0, 1, 3, 5 ,max(mat2, na.rm = TRUE)) 699 | div_cols = div_cols[c(1,2,3,7,8,10,11)] 700 | 701 | mat2 = mat2[order(rowMeans(mat2, na.rm = TRUE), decreasing = TRUE), ] 702 | 703 | pdf("./Figures/lncRNA_heatmap.pdf") 704 | pheatmap(mat2, cluster_rows = FALSE , cluster_cols = TRUE, labels_row = "", breaks = mat_breaks, color = div_cols, legend_breaks = c(-3, -1,0, 1, 3,5, max(mat2, na.rm = TRUE)), legend_labels = c(-3, -1, 0, 1, 3,5, "L2FC\n"), cex = 1.2 ) 705 | dev.off() 706 | 707 | ``` 708 | 709 | 710 | ## Genomic predictions 711 | 712 | ```{r, genomic_analysis, warning = FALSE} 713 | Gtrans = GetSeq(unlist(annots$transcript_id), mart) 714 | Gtrans = Gtrans[is.na(match(Gtrans$ensembl_transcript_id, rownames(res$train))), ] 715 | Gdf = FeatureExtract(Gtrans) 716 | preds = DeepLncRNA(Gdf) 717 | Gdf = cbind(preds, Gdf) 718 | Gdf$transcript_biotype = Gtrans$transcript_biotype 719 | dim(Gdf) 720 | 721 | ## check overall predictions 722 | table(preds$predict) 723 | 724 | 725 | pos = Gdf %>% 726 | group_by(transcript_biotype) %>% 727 | summarise(avg = (sum(predict == "Nuclear")/n())*100, count = n()) %>% 728 | filter(count > 20) %>% 729 | arrange(desc(avg)) %>% 730 | dplyr::select(transcript_biotype) 731 | pos = as.character(pos$transcript_biotype) 732 | 733 | Gdf %>% 734 | group_by(transcript_biotype) %>% 735 | summarise(avg = (sum(predict == "Nuclear")/n())*100, count = n()) %>% 736 | filter(count > 20) %>% 737 | arrange(desc(avg)) %>% 738 | ggplot( aes(x = as.factor(transcript_biotype), avg, fill = as.factor(transcript_biotype))) + 739 | geom_bar(stat="identity", position = "dodge") + 740 | xlab("") + 741 | ylab("% Nuclear") + 742 | coord_flip() + 743 | geom_hline(yintercept = 50, col = "red", lwd = 1) + 744 | scale_x_discrete(limits = pos) + 745 | guides(fill=FALSE) + 746 | theme_bw(base_size = 18) 747 | ggsave("./Figures/genomic_biotype_loc.pdf") 748 | 749 | ``` 750 | 751 | ## Predictions on lncRNAs with known localizations 752 | 753 | ```{r, known_locs} 754 | library(dplyr) 755 | library(reshape2) 756 | library(ggplot2) 757 | # annots ------------------------------------------------------------------ 758 | known = read.csv("./Data/annotated_lncRNAs.csv") 759 | source("./src/DeepLncRNA.R") 760 | trans = Gene2Transcript(known$ID, mart) 761 | seqs = GetSeq(trans$ensembl_transcript_id, mart) 762 | 763 | mousemart = biomaRt::useMart("ensembl", dataset = "mmusculus_gene_ensembl") 764 | transM = Gene2Transcript(known$ID[known$Species == "Mouse"], mart = mousemart) 765 | seqM = GetSeq(transM$ensembl_transcript_id, mart = mousemart) 766 | 767 | Borg = seqM 768 | Borg$ensembl_transcript_id = "BORG" 769 | Borg$cdna = stringr::str_replace_all(known$seq[6], "\n","") 770 | Borg$transcript_length = nchar(as.character(Borg$cdna)) 771 | Borg$GC_content = sum(oligonucleotideFrequency(DNAString(Borg$cdna), 1)[c(2,3)])/ sum(oligonucleotideFrequency(DNAString(Borg$cdna), 1)) 772 | 773 | 774 | fullseq = rbind(Borg,seqM,seqs) 775 | fullseq$chromosome_name[1:2] = 0 ## set to zero bc not on human chroms (mouse lncRNAs) 776 | fullseq = fullseq %>% filter(transcript_biotype != "protein_coding") %>% 777 | filter(transcript_biotype != "nonsense_mediated_decay") %>% 778 | filter(transcript_length >= 200) 779 | 780 | df = FeatureExtract(fullseq) 781 | 782 | trans = rbind(transM, trans, c("BORG","BORG","lincRNA")) 783 | 784 | ################ 785 | #build new DNN excluding all known LncRNAs from train/valid set 786 | res$train = res$train[is.na(match(rownames(res$train), trans$ensembl_transcript_id)), ] 787 | res$validate = res$validate[is.na(match(rownames(res$validate), trans$ensembl_transcript_id)), ] 788 | 789 | library(h2o) 790 | localH2O = h2o.init(ip="localhost", port = 54321, startH2O = TRUE, nthreads = 2, max_mem_size = "8G") 791 | h2o.no_progress() 792 | train_hex = as.h2o(rbind(res$train[ ,-1], res$validate[ ,-1])) 793 | 794 | 795 | DNN = h2o.deeplearning( 796 | training_frame=train_hex, 797 | validation_frame = valid_hex, 798 | x=1:1582, 799 | y=1583, 800 | epochs= 2000, 801 | stopping_metric="misclassification", 802 | stopping_tolerance=1e-3, 803 | stopping_rounds=10, 804 | activation = "RectifierWithDropout", 805 | hidden = c(32,16,8), 806 | input_dropout_ratio = 0.4, 807 | l1 = 1e-5, 808 | l2 = 1e-4) 809 | 810 | preds = predict(DNN, as.h2o(df)) 811 | preds = as.data.frame(preds) 812 | rownames(preds) = df$ensembl_transcript_id 813 | 814 | preds$gene = trans$ensembl_gene_id[match(rownames(preds), trans$ensembl_transcript_id)] 815 | preds$name = known$Name[match(preds$gene, known$ID)] 816 | preds$Loc = known$Localized[match(preds$gene, known$ID)] 817 | 818 | meds = preds %>% 819 | group_by(gene) %>% 820 | summarise(Nuclear = sum(predict == "Nuclear")/n()) 821 | 822 | meds$Loc = known$Localized[match(meds$gene, known$ID)] 823 | meds = meds[order(meds$Loc), ] 824 | meds$Cytosol = 1-meds$Nuclear 825 | nams= known$Name[match( meds$gene, known$ID)] 826 | nams = nams[!is.na(nams)] 827 | meds$Name = nams 828 | 829 | medL = melt(meds[,c(2,4,5)], id.vars = "Name") 830 | 831 | colvec = rep("red", nrow(meds)) 832 | colvec[meds$Loc == "Cytosol"] = "blue" 833 | colvec[meds$Loc == "Dual"] = "black" 834 | 835 | ggplot(medL, aes(x = Name, value, fill = as.factor(variable))) + 836 | geom_bar(stat="identity") + 837 | xlab("") + 838 | ylab("Percent Localized") + 839 | coord_flip() + 840 | scale_x_discrete(limits = meds$Name) + 841 | scale_fill_discrete(name = "Fraction") + 842 | theme_bw() + 843 | theme(axis.text.y=element_text(colour = colvec, size = 12)) 844 | ggsave("./Figures/annotated_lncRNAs.pdf", width = 5, height = 7, units = "in") 845 | 846 | ``` 847 | ## LncLocator comparison 848 | ```{r, LncLocator_comparison} 849 | 850 | # Parse LncRNAs from LncLocator ------------------------------------------- 851 | # source("https://bioconductor.org/biocLite.R") 852 | # biocLite("seqinr") 853 | 854 | library(stringr) 855 | library(seqinr) 856 | library(Biostrings) 857 | cyto = read.fasta("./Data/LncLocator/Cytosol", as.string = TRUE) 858 | nuc = read.fasta("./Data/LncLocator/Nucleus", as.string = TRUE) 859 | seqs =c( nuc, cyto) 860 | nucnames = unlist(getAnnot(nuc)) 861 | cytonames = unlist(getAnnot(cyto)) 862 | 863 | allnames = c(nucnames, cytonames) 864 | NRs = grep( "NR_*", allnames) 865 | refseq = str_extract( allnames[NRs], "NR_\\d*") ##get Refseq IDs 866 | refseq2 = str_extract( allnames, "NM_\\d*") ##get Refseq IDs 867 | refseq2 = refseq2[!is.na(refseq2)] 868 | 869 | ensem= str_extract( allnames, "ENST\\d*") ##get Ensembl IDs 870 | ensem = ensem[!is.na(ensem)] 871 | 872 | fullnames = c(refseq, refseq2, ensem) 873 | 874 | ## Get transcript biotype and chromosome if available 875 | mart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl") 876 | map = biomaRt::getBM(mart = mart, attributes = c( "gene_biotype","refseq_ncrna", "chromosome_name"), filters = "refseq_ncrna", values = refseq) 877 | mapNM = biomaRt::getBM(mart = mart, attributes = c( "gene_biotype","refseq_ncrna", "chromosome_name"), filters = "refseq_mrna", values = refseq2) 878 | map2 = biomaRt::getBM(mart = mart, attributes = c( "gene_biotype","ensembl_transcript_id" ,"chromosome_name"), filters = "ensembl_transcript_id", values = ensem) 879 | colnames(map)= c("gene_biotype","ID", "chromosome_name") 880 | colnames(mapNM)= c("gene_biotype","ID", "chromosome_name") 881 | colnames(map2)= c("gene_biotype","ID", "chromosome_name") 882 | maps = rbind(map, mapNM, map2) 883 | maps = maps[nchar(maps$chromosome_name) <3, ] 884 | maps = maps[!is.na(maps$ID), ] 885 | 886 | #Loop through to make DF 887 | fullnames = data.frame("IDs" = c(refseq, refseq2, ensem), transcript_biotype = "", chromosome_name = "",GC_content= 0, cdna = "", stringsAsFactors = FALSE) 888 | for (i in 1:nrow(fullnames)){ 889 | 890 | bio = maps$gene_biotype[maps$ID == fullnames$IDs[i]] 891 | if (length(bio) != 0 ){ 892 | fullnames$transcript_biotype[i] = bio 893 | } else {fullnames$transcript_biotype[i] = NA} 894 | 895 | chrom = maps$chromosome_name[maps$ID == fullnames$IDs[i]] 896 | if (length(chrom) != 0 ){ 897 | fullnames$chromosome[i] = chrom 898 | } else {fullnames$transcript_biotype[i] = NA} 899 | 900 | fullnames$cdna[i] = toupper(as.character(seqs[grepl(fullnames$IDs[i], allnames)])) 901 | fullnames$GC_content[i] = sum(oligonucleotideFrequency(DNAString(fullnames$cdna[i]), 1)[c(2,3)])/ sum(oligonucleotideFrequency(DNAString(fullnames$cdna[i]), 1)) 902 | } 903 | fullnames$transcript_length = as.numeric(lapply(fullnames$cdna, nchar)) 904 | fullnames = fullnames[ ,colnames(fullnames)!= "chromosome"] 905 | 906 | 907 | allseqs = data.frame("IDs" = c(allnames), transcript_biotype = "", chromosome_name = "",GC_content= 0, cdna = "", stringsAsFactors = FALSE) 908 | for (i in 1:nrow(allseqs)) { 909 | allseqs$IDs[i] = allnames[i] 910 | allseqs$cdna[i] = toupper(as.character(seqs[allseqs$IDs[i] == allnames])) 911 | allseqs$GC_content[i] = sum(oligonucleotideFrequency(DNAString(allseqs$cdna[i]), 1)[c(2,3)])/ sum(oligonucleotideFrequency(DNAString(allseqs$cdna[i]), 1)) 912 | } 913 | allseqs$transcript_length = as.numeric(lapply(allseqs$cdna, nchar)) 914 | 915 | ## FIlter out seqs from allseqs for which we got genomic features 916 | for(i in fullnames$IDs){ 917 | allseqs = allseqs[!grepl(i, allseqs$IDs), ] 918 | } 919 | 920 | master = rbind(fullnames, allseqs) 921 | 922 | master$Loc = "" 923 | for (i in 1:nrow(master)){ 924 | ID = master$IDs[i] 925 | if (sum(grepl(ID, cytonames)) == 1 ){master$Loc[i] = "Cytosol" 926 | }else if (sum(grepl(ID, nucnames)) == 1 ){master$Loc[i] = "Nuclear" 927 | }else if (sum(ID == nucnames)==1) { master$Loc[i] = "Nuclear" 928 | }else if (sum(ID == cytonames)==1) { master$Loc[i] = "Cytosol" } 929 | } 930 | 931 | filt = is.na(match(master$IDs, c(rownames(res$train), rownames(res$validate) )) ) 932 | master = master[filt, ] 933 | 934 | source("./src/DeepLncRNA.R") 935 | lncs = FeatureExtract(master) 936 | lncs$Loc 937 | ## Remove any lncRNAs present in training or validation data 938 | 939 | preds = DeepLncRNA(lncs, lncs$IDs) 940 | 941 | confMat = caret::confusionMatrix(data = preds$predict, reference = as.factor(master$Loc), positive = "Nuclear") 942 | ##Lnclocator values from -- Cao, et al 2018 (Fig 7) 943 | df = data.frame("DeepLncRNA" = c(spec, sens), "LncLocator" = c( .47, .38), "Metric" = c("Specificity","Sensitivity")) 944 | spec = confMat$table[1,1]/(confMat$table[1,1] + confMat$table[2,1]) 945 | sens = confMat$table[2,2]/(confMat$table[2,2] + confMat$table[1,2]) 946 | 947 | df = melt(df, "Metric") 948 | ggplot(data = df, aes(x = as.factor(variable), value , fill = Metric)) + 949 | geom_bar(stat="identity", position = "dodge") + 950 | theme_bw() + 951 | theme(axis.text.x=element_text( size = 14)) + 952 | theme(axis.text.y=element_text( size = 14) ) + 953 | xlab("") + 954 | ylab("") + 955 | theme(legend.text=element_text(size=15)) 956 | ggsave("./Figures/Lnclocator.pdf") 957 | 958 | sink("./Data/LncLocator_conf.txt") 959 | print(confMat) 960 | sink() 961 | 962 | ``` 963 | 964 | 965 | 966 | 967 | --------------------------------------------------------------------------------