├── .gitattributes ├── .gitignore ├── LICENSE ├── ProFET ├── Output │ ├── NPP_CleavedSP-TopFeaturesImportanceRFE_Figure.png │ ├── NPP_TopFeaturesV4.png │ ├── NppCM.png │ ├── Output-Scores.xls │ ├── Output-Scores.xlsx │ ├── OutputData-Cleaned.xlsx │ ├── OutputData-CleanedV2.xlsx │ ├── OutputData.xlsx │ ├── OutputRes_basic_1.png │ ├── ROC.png │ ├── ROC_Curve.ipynb │ ├── ResultsProt2FeatDatasets.doc │ ├── Thermophiles-TopFeaturesImportancefigure_1.png │ ├── Thermophiles-TopFeaturesImportancefigure_1.svg │ ├── ThermophilesCM.png │ ├── Thermophiles_CompositionProfiler-AAComp.png │ ├── Thermophiles_FeatCountPerfGraph.png │ ├── VisualizebestFeatHist.py │ ├── Workflow.png │ └── checkf1.py └── feat_extract │ ├── AAComposition.py │ ├── AAScales.py │ ├── AAlphabets.py │ ├── CTD_pro.py │ ├── Disorder.py │ ├── FastaFilter.py │ ├── FeatureGen.py │ ├── GetPredictorPerf.py │ ├── GetResults.py │ ├── Model_Parameters_CV.py │ ├── Model_trainer.py │ ├── OutPutRes.py │ ├── PipeTasks.py │ ├── ProFET.py │ ├── ProtFeat.py │ ├── SciKit_plot_roc.py │ ├── VisualizeBestFeatures.py │ ├── VisualizebestFeatHist.py │ ├── __init__.py │ ├── params.py │ ├── pipeline.py │ ├── plot_roc.py │ ├── readme.txt │ └── test_seq │ ├── BenchM │ ├── dna-rna-binding │ │ ├── DNA-binding │ │ │ ├── DNA-Bind-alt.fasta │ │ │ └── DNAalter_nonbind.fasta │ │ └── RNA-Binding │ │ │ ├── NEGRNA.fasta │ │ │ └── RNABinding.fasta │ └── scop │ │ ├── Astral_SCOPe_2.04_Orig_0.3ID.fasta │ │ ├── RegExSCOP.txt │ │ ├── scopFolds │ │ └── Scope_Folds_Filt_30ID.fasta │ │ └── supfam_3 │ │ ├── FILTSCOPe_2.04_fam_0.3ID.fasta │ │ └── SCOPe_2.04_fam_0.3ID.fasta │ ├── Extracellular │ ├── NOT-secreted_NOT-extracellular_reviewed_taxon-Tetrapoda_fragment-no_id-0.5.fasta │ └── location-secreted_keyword-AKW-0964_reviewed_taxon-Tetrapoda_fragment-no_id-0.9.fasta │ ├── Mamm_Organellas │ ├── Mammal_Lysosome_0.9.fasta │ ├── Mammal_Mitochondrion_5.fasta │ ├── Mammal_Nucleolus_0.9.fasta │ ├── Mammal_Secreted_05.fasta │ ├── Mammal_melanosome_0.9.fasta │ └── Mammal_peroxisome9.fasta │ ├── NP │ ├── NEG_SPCleaved.fasta │ ├── NP+SP+Negs_BigBalanced │ │ ├── NEG_+SP+TMD.fasta │ │ ├── NEG_+SP-TMD.fasta │ │ ├── NP+.fasta │ │ ├── neg_+TMD_30.fasta │ │ └── neg_-TMD_30.fasta │ ├── NP+SPCleaved.fasta │ └── SP_CleavedNP+Neg │ │ ├── NP.fasta │ │ ├── Neg.fasta │ │ └── files.txt │ └── Viri │ ├── Host-Bac-Vert-0.5 │ ├── Virii_ViralHost-Bacteria_Reviewed_Non-Fragment_0.5ID.fasta │ └── Virii_ViralHost-Vertebrates_Reviewed_0.5ID.fasta │ ├── Host-Bac-Vert-0.9 │ ├── Virii_ViralHost-Bacteria_Reviewed_Non-Fragment_0.9ID.fasta │ └── Virii_ViralHost-Vertebrates_Reviewed_0.9ID.fasta │ └── Viri-Capsids │ ├── Viri_Capsid-Proteins_Host-Bacteria_0.9.fasta │ ├── Viri_Capsid-Proteins_Host-Metazoa_0.9.fasta │ └── Viri_Capsid-Proteins_Host-Viridiplantae_0.9.fasta ├── README.md └── fastas ├── Benchmarks ├── CATH │ ├── CATH-README.file_formats.txt │ └── Cath.DataSet.0.3ID.fasta ├── DNA-RNA-Binding │ ├── DNA-binding │ │ ├── DNA-Bind-alt.fasta │ │ └── DNAalter_nonbind.fasta │ └── RNA-Binding │ │ ├── NEGRNA.fasta │ │ └── RNABinding.fasta ├── LocTree3 │ ├── archaea.59.fasta │ ├── bact │ │ └── FILTbacteria.455.fasta │ ├── bacteria.479.fasta │ ├── bactloc_30id.fasta │ └── euk │ │ └── eukaryota.1682.fasta ├── PSORTb_3.0 │ ├── Gram-negative │ │ ├── CytoplasmicMembrane_1607.fasta │ │ ├── Cytoplasmic_5025.fasta │ │ ├── Extracellular_419.fasta │ │ ├── Outer Membrane_541.fasta │ │ └── Periplasmic_437.fasta │ └── Gram-positive │ │ ├── FILTcellwall+3_0.fasta │ │ ├── FILTcytoplasmic+3_0.fasta │ │ ├── FILTextracellular+3_0.fasta │ │ ├── cellwall+3_0.fasta │ │ ├── cytoplasmic+3_0.fasta │ │ └── extracellular+3_0.fasta ├── SCOP │ ├── HPFP_class │ │ ├── train_a.fasta │ │ ├── train_b.fasta │ │ ├── train_c.fasta │ │ ├── train_d.fasta │ │ ├── train_e.fasta │ │ ├── train_f.fasta │ │ └── train_g.fasta │ ├── RegExSCOP.txt │ ├── SCOP10.fasta │ ├── SCOP20.fa │ ├── SCOPe_Orig_0.3ID.fasta │ ├── SClass │ │ └── SCOPClass10.fasta │ └── Sfolds │ │ └── FILTSCOPe_Folds_03ID.fasta ├── SCOPe_Folds_03ID.fasta ├── SOURCES.txt └── Thermophiles │ ├── -.fasta │ ├── Therm.fasta │ └── ThermophilesTopFeats.png ├── Locations ├── Gnathostomes_Vert │ ├── Mitochondrion_NOT-Nucleus_Not-ECM_0.9_Gnath.fasta │ ├── PBodies_1.0_NOT-Nucleus_Gnath.fasta │ ├── Perixosome_1.0_Gnath.fasta │ ├── lysosome_1.0_gnath.fasta │ ├── melanosome_1.0_not-nucleus_gnath.fasta │ ├── nucleolus_1.0_gnath.fasta │ ├── nucleus_and-cytoplasm_not-nucleolus_not-ecm_0.9_gnath.fasta │ ├── nucleus_not-cytoplasm_not-nucleolus_not-ecm_0.5_gnath.fasta │ └── secreted_and-extracellular_not-nucleus_0.5_gnath.fasta └── Mamm_Organellas │ ├── Mammal_Lysosome_0.9.fasta │ ├── Mammal_Mitochondrion-LOC_Subcell-Mitochondrion_0.9.fasta │ ├── Mammal_Nucleolus_0.9.fasta │ ├── Mammal_melanosome_0.9.fasta │ └── Mammal_peroxisome_NOT-Mitochondrion_0.9.fasta ├── NP ├── 20NP_Cnid_New │ ├── CnidValidation │ │ └── SPCleaved_UniProtAnnotatedNoisy-PotentialCnidariaNP.fasta │ └── Train │ │ ├── NEG_20_SP.fasta │ │ └── SPc_+NPP.fasta ├── NP-Vs-Hormones │ ├── hormone_precursors+sp_+reviewed_notneuropeptides_notreceptor_0.9.fasta │ └── neuropeptide_notkw-hormone_precursors+sp_+reviewed_notreceptor_0.9.fasta ├── NPP+Negs │ ├── +SP_NP+Negs_smallBalanced_UniProt │ │ ├── neg_cdhit_+sp_+tmd_metazoa_notnp_notfragment_900.fasta │ │ ├── neg_cdhit_+sp_-tmd_metazoa_notnp_notfragment_1790.fasta │ │ └── uniprot_np+_+sp_not-tmd_+metazoa_all_1.0_511.fasta │ ├── NP+SP_+Negs_Large+Balanced │ │ ├── np+sp.fasta │ │ ├── unip_+sp_+tmd_+precursor_metazoa_notnp_notfragment_2131_0.5id.fasta │ │ └── unip_+sp_-tmd_metazoa_notnp_notfragment_4013_0.5-id.fasta │ └── sample-np+_+sp_-tmd_+metazoa_0.3_176.fasta ├── Neuropeptides+ _ 8.2014_Uniprot │ ├── More_Data │ │ ├── uniref-LENGTHS_NP-KW_1.0.tsv │ │ └── uniref-LENGTHS_propep_cleavage_SP+NP-KW_1.0.tsv │ ├── NEG_NotNP_+SP_-TMD_0.5.fasta │ ├── Search-strings.txt │ ├── propep_cleavage_SP+NP-KW_1.0.fasta │ └── uniprot-NP_KW_.9.fasta ├── NotNPP_NotProPep_Neg_Secreted_2015_30ID.fasta ├── NotNPP_NotProPep_Neg_Secreted_2015_all.fasta ├── Organism-Proteomes │ └── Nematostella │ │ ├── Nematostella_Not-Fragment_Uniprot_1.0.1.fasta │ │ ├── Nematostella_Not-Fragment_Uniprot_1.0.4.fasta │ │ ├── nematostella_all_not-fragment_uniprot_1.0.fasta │ │ ├── nematostella_not-fragment_uniprot_1.0.0.fasta │ │ ├── nematostella_not-fragment_uniprot_1.0.2.fasta │ │ ├── nematostella_not-fragment_uniprot_1.0.3.fasta │ │ ├── nematostella_not-fragment_uniprot_1.0.5.fasta │ │ └── nematostella_not-fragment_uniprot_1.0.6.fasta ├── SP_Cleaved+NP+Neg_Big │ ├── +.fasta │ └── -.fasta └── Train │ ├── NEG_+SP_+TMD_Metazoa_NotNP_NotFragment_0.9ID.fasta │ ├── NEG_NOT-NP_Membrane+SP+DBCleavage+Non-Fragment+0.9.fasta │ ├── neg__reference_not-sp_+tmd_metazoa_notnp_notfragment_0.5id.fasta │ ├── neg_not-np_not-hormone_+sp+dbcleavage+non-fragment+0.9.fasta │ └── npp+sp_uniprot+ncbi_0.95.fasta ├── Ribosomes ├── RibArch4.fasta ├── RibBact2.fasta └── RibEuk3.fasta └── Viruses ├── Viri-Capsids ├── NOTE.txt ├── Viri-Doublestranded_Capsid │ ├── reviewed_host-metazoa_capsid_location-virion_not+precursor+not-polyprotein_1.0.fasta │ └── reviewed_host-notmetazoa_capsid_location-virion_not+precursor+not-polyprotein_1.0.fasta ├── Viri_Capsid-Proteins_Host-Viridiplantae_0.9.fasta ├── viri_capsid-proteins_host-bacteria_0.9.fasta └── viri_capsid-proteins_host-metazoa_0.9.fasta ├── Viri-Class ├── Classes │ ├── dsdna+norna_reviewed_0.5.fasta │ ├── dsrna_reviewed_1.0.fasta │ ├── retroviruses_reviewed_0.9.fasta │ ├── ssdna_reviewed_1.0.fasta │ └── ssrna_reviewed_0.9.fasta ├── Viri-Capsid-Classes_New │ ├── Vir-Capsid_dsDNA+Euk_all.fasta │ ├── Vir-Capsid_dsRNA+Euk_all.fasta │ ├── Vir-Capsid_ssDNA+Euk_50.fasta │ ├── Vir-Capsid_ssRNA+Euk_all.fasta │ ├── dsDNA_45.fasta │ ├── dsRNA_45.fasta │ └── ssRNA_45.fasta ├── dsdna+norna_reviewed_0.5.fasta ├── dsdna+norna_reviewed_0.9.fasta ├── dsrna_reviewed_1.0.fasta ├── retroviruses_reviewed_0.9.fasta ├── ssdna_reviewed_1.0.fasta ├── ssrna+nodna+negativestrand_reviewed_0.9.fasta ├── ssrna+nodna+positivestrand_reviewed_0.9.fasta └── ssrna_reviewed_0.9.fasta └── Viri-Host ├── Capsids-Host ├── Viri_Capsid-Proteins_Host-Bacteria_0.9.fasta ├── Viri_Capsid-Proteins_Host-Metazoa_0.1.fasta └── Viri_Capsid_Host-Viridi_0.3.fasta ├── Viri-BV-0.5 ├── ArcheaHost_50ID.fasta ├── ViriHost_Vert_30ID.fasta └── virii_viralhost-bacteria_reviewed_non-fragment_0.5id.fasta ├── Virii_ViralHost-Vertebrates_Reviewed_1.0ID.fasta ├── viralhost-archaea_reviewed_1.0id.fasta ├── viralhost-archaea_reviewed_1.0id_2.fasta ├── virii_viralhost-bacteria_all_non-fragment_0.9id.fasta ├── virii_viralhost-bacteria_reviewed_non-fragment_0.5id.fasta ├── virii_viralhost-bacteria_reviewed_non-fragment_1.0id.fasta ├── virii_viralhost-ecoli_reviewed_1.0id.fasta └── virii_viralhost-vertebrates_reviewed_0.5id.fasta /.gitattributes: -------------------------------------------------------------------------------- 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