├── Descriptor_headers.pdf ├── Feature_Description.pdf ├── LICENSE ├── Pfeature_Manual.pdf ├── PyLib ├── Functions_Tables.pdf ├── Pfeature.zip └── README.md ├── README.md ├── Standalone ├── Data │ ├── AAIndexNames.csv │ ├── Grantham.csv │ ├── PhysicoChemical.csv │ ├── README.md │ ├── Schneider-Wrede.csv │ ├── aa_attr_group.csv │ ├── aaind.txt │ ├── aaindex.csv │ ├── aaindices.csv │ ├── atom.csv │ ├── bin_di.csv │ ├── bonds.csv │ ├── can_pat.csv │ ├── data │ └── z_aaindex.csv ├── LICENSE ├── Pfeature_Descriptors.pdf ├── README.md ├── README.txt ├── Requirement.txt ├── Screenshot.png ├── envfile ├── pfeature_bin.py ├── pfeature_comp.py ├── pfeature_pssm.py ├── pfeature_standalone.zip ├── protein.fa └── protein.seq └── scripts ├── Pfeature_scripts.zip └── readme /Descriptor_headers.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raghavagps/Pfeature/1117d4c9712a7d230ed0e0026be8d9a2d859e978/Descriptor_headers.pdf -------------------------------------------------------------------------------- /Feature_Description.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raghavagps/Pfeature/1117d4c9712a7d230ed0e0026be8d9a2d859e978/Feature_Description.pdf -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986 3 | size 35149 4 | -------------------------------------------------------------------------------- /Pfeature_Manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raghavagps/Pfeature/1117d4c9712a7d230ed0e0026be8d9a2d859e978/Pfeature_Manual.pdf -------------------------------------------------------------------------------- /PyLib/Functions_Tables.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raghavagps/Pfeature/1117d4c9712a7d230ed0e0026be8d9a2d859e978/PyLib/Functions_Tables.pdf -------------------------------------------------------------------------------- /PyLib/Pfeature.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raghavagps/Pfeature/1117d4c9712a7d230ed0e0026be8d9a2d859e978/PyLib/Pfeature.zip -------------------------------------------------------------------------------- /PyLib/README.md: -------------------------------------------------------------------------------- 1 | Library Package of Pfeature
2 | =============================== 3 | 4 | INTRODUCTION
5 | ------------------ 6 | Pfeature is a standalone software package for computing wide range of protein and peptides features from their amino acid sequence. It has the following five major modules for computing protein features based on; 7 | - Composition 8 | - Binary profiles 9 | - Evolutionary information 10 | - Structure 11 | - Pattern 12 | 13 | We have developed number of forms of Pfeature that include: 14 | - A web server that uses Pfeature functions via web interface from https://webs.iiitd.edu.in/raghava/pfeature 15 | - Standalone version of Pfeature 16 | - Library of python for Pfeature and iv) Python scripts for computing features. 17 | 18 | INSTALLATION
19 | --------------- 20 | Installation of Pfeature is simple as explained below: 21 | 22 | On Microsoft Windows: 23 | 1. Download Pfeature.zip from https://github.com/raghavagps/Pfeature/blob/master/PyLib/Pfeature.zip 24 | 2. extract or uncompress the Pfeature.zip 25 | 3. change directory to Pfeature 26 | 4. Run the command: python3 setup.py install 27 | 28 | On Mac/Linux: 29 | 1. Download Pfeature.zip from https://github.com/raghavagps/Pfeature/blob/master/PyLib/Pfeature.zip 30 | 2. unzip the Pfeature.zip 31 | 3. change directory to Pfeature 32 | 4. Run the command: python3 setup.py install or sudo python3 setup.py install 33 | 34 | On Centos: 35 | 1. Download Pfeature.zip from https://github.com/raghavagps/Pfeature/blob/master/PyLib/Pfeature.zip 36 | 2. unzip the Pfeature.zip 37 | 3. change directory to Pfeature 38 | 4. Run the command: python3 setup.py install 39 | 40 | 41 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Pfeature: Computation of features of peptides and proteins 2 | 3 | ## Introduction 4 | Pfeature is a comprehensive software developed for computing wide range of protein/peptide features that have been discovered over the past decades. It has the following five major modules for computing protein features based on; i) Composition, ii) Binary profiles, iii) Evolutionary information iv) Structure and v) Pattern. The composition based module allows user to compute; i) Simple compositions like amino acid, dipeptide, tripeptide; ii) Physicochemical properties based compositions; iii) Repeats and distribution of amino acids; iv) Shannon entropy to measure the low complexity regions; iv) Miscellaneous compositions like pseudo amino acid, autocorrelation, conjoint triad, quasi-sequence order. Binary profile of amino acid sequence provides complete information including order of residues or type of residues, which is not possible with composition based features. Thus, binary profile can be used to annotate protein at residue level. It is well established in literature that sequence profile based on evolutionary information provides more information then sequence itself. 5 | 6 | We have developed number of isoforms of Pfeature that include: i) A web server that uses Pfeature functions via web interface from https://webs.iiitd.edu.in/raghava/pfeature/ ; ii) Standalone version of Pfeature; iii) Library of python for Pfeature and iv) Python scripts for computing features. 7 | 8 | ## Documentation 9 | One can read more about subroutines developed under Pfeature to compute wide range of proteins and peptide features from https://github.com/raghavagps/Pfeature/blob/master/Pfeature_Man.pdf . Further information is available from help page of web site https://webs.iiitd.edu.in/raghava/pfeature/help.php 10 | 11 | ## Web Service for Pfeature 12 | A web server for computing wide range of protein and peptides features from their amino acid sequences. Following are main menus for computing features; i) Composition-based features, ii) Binary profile of sequences, iii) evolutionary information based features, iv) structural descriptors,and v) pattern based descriptors, for a group of protein/peptide sequences. Additionally, users will also be able to generate these features for sub-parts of protein/peptide sequences. Pfeature will be helpful to annotate structure, function and therapeutic properties of proteins/peptides. 13 | 14 | **Available from URL: https://webs.iiitd.edu.in/raghava/pfeature/** 15 | ## PIP Installation 16 | PIP version is also available for easy installation and usage of this tool. The following command is required to install the package 17 | ``` 18 | pip install pfeature 19 | ``` 20 | To know about the available option for the pip package, type the following command: 21 | ``` 22 | pfeature -h 23 | ``` 24 | 25 | ### Installation of Pfeature Library 26 | 27 | ### Prerequisite 28 | The prerequisite to run the python library is pandas, numpy and python version above 3.6 29 | pandas can be installed using following command: pip3 install pandas 30 | numpy can be installed using following command: pip3 install numpy 31 | 32 | ### Steps for setting library 33 | It has been tested on wide range of platforms that include Apple MAC, Windows and Linux (Ubuntu,Fedora). After installing pandas and numpy user can install using following commands
34 | 35 | 1. Download Pfeature from https://github.com/raghavagps/Pfeature/blob/master/PyLib/Pfeature.zip
36 | 2. Extract or uncompress Pfeature.zip
37 | 3. cd Pfeature
38 | 4. python setup.py install
39 | 40 | ## Standalone Package of Pfeature 41 | In order to facilitate users, we created a single program of Pfeature which computes individual as well as, all possible descriptors for a protein/peptide sequence. 42 | It has been tested on wide range of platforms that include Apple MAC, Windows and Linux (Ubuntu,Fedora). After installing pandas and numpy user can install using following commands
43 | 44 | 1. Download Pfeature from https://github.com/raghavagps/Pfeature/blob/master/Standalone/pfeature_standalone.zip
45 | 2. Extract or uncompress pfeature_standalone.zip
46 | 3. cd pfeature_standalone
47 | 48 | # Reference 49 | Pande et al (2022) Pfeature: A Tool for Computing Wide Range of Protein Features and Building Prediction Models. J Comput Biol. 2022 Oct 13. doi: 10.1089/cmb.2022.0241. 50 | -------------------------------------------------------------------------------- /Standalone/Data/AAIndexNames.csv: -------------------------------------------------------------------------------- 1 | ANDN920101 2 | ARGP820101 3 | ARGP820102 4 | ARGP820103 5 | AURR980101 6 | AURR980102 7 | AURR980103 8 | AURR980104 9 | AURR980105 10 | AURR980106 11 | AURR980107 12 | AURR980108 13 | AURR980109 14 | AURR980110 15 | AURR980111 16 | AURR980112 17 | AURR980113 18 | AURR980114 19 | AURR980115 20 | AURR980116 21 | AURR980117 22 | AURR980118 23 | AURR980119 24 | AURR980120 25 | BAEK050101 26 | BASU050101 27 | BASU050102 28 | BASU050103 29 | BEGF750101 30 | BEGF750102 31 | BEGF750103 32 | BHAR880101 33 | BIGC670101 34 | BIOV880101 35 | BIOV880102 36 | BLAM930101 37 | BLAS910101 38 | BROC820101 39 | BROC820102 40 | BULH740101 41 | BULH740102 42 | BUNA790101 43 | BUNA790102 44 | BUNA790103 45 | BURA740101 46 | BURA740102 47 | CASG920101 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| VINM940101 521 | VINM940102 522 | VINM940103 523 | VINM940104 524 | WARP780101 525 | WEBA780101 526 | WERD780101 527 | WERD780102 528 | WERD780103 529 | WERD780104 530 | WILM950101 531 | WILM950102 532 | WILM950103 533 | WILM950104 534 | WIMW960101 535 | WOEC730101 536 | WOLR790101 537 | WOLR810101 538 | WOLS870101 539 | WOLS870102 540 | WOLS870103 541 | YUTK870101 542 | YUTK870102 543 | YUTK870103 544 | YUTK870104 545 | ZASB820101 546 | ZHOH040101 547 | ZHOH040102 548 | ZHOH040103 549 | ZIMJ680101 550 | ZIMJ680102 551 | ZIMJ680103 552 | ZIMJ680104 553 | ZIMJ680105 -------------------------------------------------------------------------------- /Standalone/Data/Grantham.csv: -------------------------------------------------------------------------------- 1 | Name,A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y,V 2 | A,0,112,111,126,195,91,107,60,86,94,96,106,84,113,27,99,58,148,112,64 3 | R,112,0,86,96,180,43,54,125,29,97,102,26,91,97,103,110,71,101,77,96 4 | N,111,86,0,23,139,46,42,80,68,149,153,94,142,158,91,46,65,174,143,133 5 | D,126,96,23,0,154,61,45,94,81,168,172,101,160,177,108,65,85,181,160,152 6 | C,195,180,139,154,0,154,170,159,174,198,198,202,196,205,169,112,149,215,194,192 7 | Q,91,43,46,61,154,0,29,87,24,109,113,53,101,116,76,68,42,130,99,96 8 | E,107,54,42,45,170,29,0,98,40,134,138,56,126,140,93,80,65,152,122,121 9 | G,60,125,80,94,159,87,98,0,98,135,138,127,127,153,42,56,59,184,147,109 10 | H,86,29,68,81,174,24,40,98,0,94,99,32,87,100,77,89,47,115,83,84 11 | I,94,97,149,168,198,109,134,135,94,0,5,102,10,21,95,142,89,61,33,29 12 | L,96,102,153,172,198,113,138,138,99,5,0,107,15,22,98,145,92,61,36,32 13 | K,106,26,94,101,202,53,56,127,32,102,107,0,95,102,103,121,78,110,85,97 14 | M,84,91,142,160,196,101,126,127,87,10,15,95,0,28,87,135,81,67,36,21 15 | F,113,97,158,177,205,116,140,153,100,21,22,102,28,0,114,155,103,40,22,50 16 | P,27,103,91,108,169,76,93,42,77,95,98,103,87,114,0,74,38,147,110,68 17 | S,99,110,46,65,112,68,80,56,89,142,145,121,135,155,74,0,58,177,144,124 18 | T,58,71,65,85,149,42,65,59,47,89,92,78,81,103,38,58,0,128,92,69 19 | W,148,101,174,181,215,130,152,184,115,61,61,110,67,40,147,177,128,0,37,88 20 | Y,112,77,143,160,194,99,122,147,83,33,36,85,36,22,110,144,92,37,0,55 21 | V,64,96,133,152,192,96,121,109,84,29,32,97,21,50,68,124,69,88,55,0 22 | -------------------------------------------------------------------------------- /Standalone/Data/PhysicoChemical.csv: -------------------------------------------------------------------------------- 1 | 0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,0,0,0,0 2 | 0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | 1,1,0,0,1,1,0,1,0,1,1,1,1,1,0,1,1,1,1,1 4 | 0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,1,1,0,0,1 5 | 1,0,0,0,1,1,0,1,0,1,1,0,1,0,0,0,0,1,1,0 6 | 1,0,0,0,0,1,0,1,0,1,0,0,1,0,0,0,0,1,0,0 7 | 0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0 8 | 0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1 9 | 0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 10 | 0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,0,0,0,0 11 | 1,1,0,0,1,1,0,1,0,1,1,1,1,1,0,1,1,1,1,1 12 | 1,1,0,0,1,0,0,1,0,1,1,0,1,0,0,0,1,1,1,0 13 | 0,0,0,0,0,0,1,0,1,0,0,1,1,0,1,0,0,0,0,0 14 | 0,0,1,1,0,1,0,0,0,0,0,0,0,1,0,1,1,0,0,0 15 | 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0 16 | 0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 17 | 1,0,0,1,0,0,1,0,1,1,1,0,0,1,1,0,0,0,0,0 18 | 0,1,0,0,1,0,0,1,0,0,0,0,0,0,0,0,1,1,1,1 19 | 0,0,1,0,0,1,0,0,0,0,0,1,1,0,0,1,0,0,0,0 20 | 1,1,0,0,1,1,0,1,0,1,0,0,0,0,0,0,0,1,1,0 21 | 0,0,1,1,0,0,0,0,1,0,0,1,1,1,0,0,0,0,0,0 22 | 0,0,0,0,0,0,1,0,0,0,1,0,1,0,0,1,1,0,0,1 23 | 1,1,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0 24 | 1,1,1,0,0,1,0,0,0,0,0,1,1,0,0,1,1,1,0,0 25 | 0,0,0,1,1,0,1,1,1,1,1,0,0,1,1,0,0,0,1,1 26 | 0.24,0.84,3.98,3.11,-4.22,2.05,2.47,-3.89,2.29,-4.28,-2.85,3.05,-1.66,1.75,3.52,2.39,0.75,-2.59,-4.36,-2.54 27 | -2.32,-1.67,0.93,0.26,1.94,-4.06,1.95,-1.73,0.89,-1.3,-0.22,1.62,0.27,0.5,2.5,-1.07,-2.18,-2.64,3.94,2.44 28 | 0.6,3.71,1.93,-0.11,1.06,0.36,0.26,-1.71,-2.49,-1.49,0.47,1.04,1.84,-1.44,-3.5,1.15,-1.12,-1.54,0.59,0.43 29 | -0.14,0.18,-2.46,-3.04,0.54,-0.82,3.9,-0.84,1.49,-0.72,1.94,-1.15,0.7,-1.34,1.99,-1.39,-1.46,-0.85,3.44,0.04 30 | 1.3,-2.65,0.75,-0.25,-0.62,-0.38,0.09,0.26,0.31,0.84,-0.98,-1.61,2,0.66,-0.17,0.67,-0.4,-0.02,-1.59,-1.47 -------------------------------------------------------------------------------- /Standalone/Data/README.md: -------------------------------------------------------------------------------- 1 | # Standalone Package of Pfeature 2 | --------------------------------- 3 | ## Introduction 4 | Pfeature is a standalone software package for computing wide range of protein and peptides features from their amino acid 5 | sequence. It has the following five major modules for computing protein features based on:
6 | 13 | We have developed number of forms of Pfeature that include: 14 | 20 | 21 | -------------------------------------------------------------------------------- /Standalone/Data/Schneider-Wrede.csv: -------------------------------------------------------------------------------- 1 | Name,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y 2 | A,0,0.112,0.819,0.827,0.54,0.208,0.696,0.407,0.891,0.406,0.379,0.318,0.191,0.372,1,0.094,0.22,0.273,0.739,0.552 3 | C,0.114,0,0.847,0.838,0.437,0.32,0.66,0.304,0.887,0.301,0.277,0.324,0.157,0.341,1,0.176,0.233,0.167,0.639,0.457 4 | D,0.729,0.742,0,0.124,0.924,0.697,0.435,0.847,0.249,0.841,0.819,0.56,0.657,0.584,0.295,0.667,0.649,0.797,1,0.836 5 | E,0.79,0.788,0.133,0,0.932,0.779,0.406,0.86,0.143,0.854,0.83,0.599,0.688,0.598,0.234,0.726,0.682,0.824,1,0.837 6 | F,0.508,0.405,0.977,0.918,0,0.69,0.663,0.128,0.903,0.131,0.169,0.541,0.42,0.459,1,0.548,0.499,0.252,0.207,0.179 7 | G,0.206,0.312,0.776,0.807,0.727,0,0.769,0.592,0.894,0.591,0.557,0.381,0.323,0.467,1,0.158,0.272,0.464,0.923,0.728 8 | H,0.896,0.836,0.629,0.547,0.907,1,0,0.848,0.566,0.842,0.825,0.754,0.777,0.716,0.697,0.865,0.834,0.831,0.981,0.821 9 | I,0.403,0.296,0.942,0.891,0.134,0.592,0.652,0,0.892,0.013,0.057,0.457,0.311,0.383,1,0.443,0.396,0.133,0.339,0.213 10 | K,0.889,0.871,0.279,0.149,0.957,0.9,0.438,0.899,0,0.892,0.871,0.667,0.757,0.639,0.154,0.825,0.759,0.882,1,0.848 11 | L,0.405,0.296,0.944,0.892,0.139,0.596,0.653,0.013,0.893,0,0.062,0.452,0.309,0.376,1,0.443,0.397,0.133,0.341,0.205 12 | M,0.383,0.276,0.932,0.879,0.182,0.569,0.648,0.058,0.884,0.062,0,0.447,0.285,0.372,1,0.417,0.358,0.12,0.391,0.255 13 | N,0.424,0.425,0.838,0.835,0.766,0.512,0.78,0.615,0.891,0.603,0.588,0,0.266,0.175,1,0.361,0.368,0.503,0.945,0.641 14 | P,0.22,0.179,0.852,0.831,0.515,0.376,0.696,0.363,0.875,0.357,0.326,0.231,0,0.228,1,0.196,0.161,0.244,0.72,0.481 15 | Q,0.512,0.462,0.903,0.861,0.671,0.648,0.765,0.532,0.881,0.518,0.505,0.181,0.272,0,1,0.461,0.389,0.464,0.831,0.522 16 | R,0.919,0.905,0.305,0.225,0.977,0.928,0.498,0.929,0.141,0.92,0.908,0.69,0.796,0.668,0,0.86,0.808,0.914,1,0.859 17 | S,0.1,0.185,0.801,0.812,0.622,0.17,0.718,0.478,0.883,0.474,0.44,0.289,0.181,0.358,1,0,0.174,0.342,0.827,0.615 18 | T,0.251,0.261,0.83,0.812,0.604,0.312,0.737,0.455,0.866,0.453,0.403,0.315,0.159,0.322,1,0.185,0,0.345,0.816,0.596 19 | V,0.275,0.165,0.9,0.867,0.269,0.471,0.649,0.135,0.889,0.134,0.12,0.38,0.212,0.339,1,0.322,0.305,0,0.472,0.31 20 | W,0.658,0.56,1,0.931,0.196,0.829,0.678,0.305,0.892,0.304,0.344,0.631,0.555,0.538,0.968,0.689,0.638,0.418,0,0.204 21 | Y,0.587,0.478,1,0.932,0.202,0.782,0.678,0.23,0.904,0.219,0.268,0.512,0.444,0.404,0.995,0.612,0.557,0.328,0.244,0 22 | -------------------------------------------------------------------------------- /Standalone/Data/aa_attr_group.csv: -------------------------------------------------------------------------------- 1 | attr 1 2 3 2 | hydrophobicity R,K,E,D,Q,N G,A,S,T,P,H,Y C,L,V,I,M,F,W 3 | normalized vander Waals volume G,A,S,T,P,D N,V,E,Q,I,L M,H,K,F,R,Y,W 4 | polarity L,I,F,W,C,M,V,Y P,A,T,G,S H,Q,R,K,N,E,D 5 | polarizability G,A,S,D,T C,P,N,V,E,Q,I,L K,M,H,F,R,Y,W 6 | charge K,R A,N,C,Q,G,H,I,L,M,F,P,S,T,W,Y,V D,E 7 | secondary structure E,A,L,M,Q,K,R,H V,I,Y,C,W,F,T G,N,P,S,D 8 | solvent accessibility A,L,F,C,G,I,V,W R,K,Q,E,N,D M,S P,T,H,Y 9 | -------------------------------------------------------------------------------- /Standalone/Data/aaind.txt: -------------------------------------------------------------------------------- 1 | ANDN920101 2 | ARGP820101 3 | ARGP820102 4 | ARGP820103 5 | AURR980101 6 | AURR980102 7 | AURR980103 8 | AURR980104 9 | AURR980105 10 | AURR980106 11 | AURR980107 12 | AURR980108 13 | AURR980109 14 | AURR980110 15 | AURR980111 16 | AURR980112 17 | AURR980113 18 | AURR980114 19 | AURR980115 20 | AURR980116 21 | AURR980117 22 | AURR980118 23 | AURR980119 24 | AURR980120 25 | BAEK050101 26 | BASU050101 27 | BASU050102 28 | BASU050103 29 | BEGF750101 30 | BEGF750102 31 | BEGF750103 32 | BHAR880101 33 | BIGC670101 34 | BIOV880101 35 | BIOV880102 36 | BLAM930101 37 | BLAS910101 38 | BROC820101 39 | BROC820102 40 | BULH740101 41 | BULH740102 42 | BUNA790101 43 | BUNA790102 44 | BUNA790103 45 | BURA740101 46 | BURA740102 47 | CASG920101 48 | CEDJ970101 49 | CEDJ970102 50 | CEDJ970103 51 | CEDJ970104 52 | CEDJ970105 53 | CHAM810101 54 | CHAM820101 55 | CHAM820102 56 | CHAM830101 57 | CHAM830102 58 | CHAM830103 59 | CHAM830104 60 | CHAM830105 61 | CHAM830106 62 | CHAM830107 63 | CHAM830108 64 | CHOC750101 65 | CHOC760101 66 | CHOC760102 67 | CHOC760103 68 | CHOC760104 69 | CHOP780101 70 | CHOP780201 71 | CHOP780202 72 | CHOP780203 73 | CHOP780204 74 | CHOP780205 75 | CHOP780206 76 | CHOP780207 77 | CHOP780208 78 | CHOP780209 79 | CHOP780210 80 | CHOP780211 81 | CHOP780212 82 | CHOP780213 83 | CHOP780214 84 | CHOP780215 85 | CHOP780216 86 | CIDH920101 87 | CIDH920102 88 | CIDH920103 89 | CIDH920104 90 | CIDH920105 91 | COHE430101 92 | CORJ870101 93 | CORJ870102 94 | CORJ870103 95 | CORJ870104 96 | CORJ870105 97 | CORJ870106 98 | CORJ870107 99 | CORJ870108 100 | COSI940101 101 | COWR900101 102 | CRAJ730101 103 | CRAJ730102 104 | CRAJ730103 105 | DAWD720101 106 | DAYM780101 107 | DAYM780201 108 | DESM900101 109 | DESM900102 110 | DIGM050101 111 | EISD840101 112 | EISD860101 113 | EISD860102 114 | EISD860103 115 | ENGD860101 116 | FASG760101 117 | FASG760102 118 | FASG760103 119 | FASG760104 120 | FASG760105 121 | FASG890101 122 | FAUJ830101 123 | FAUJ880101 124 | FAUJ880102 125 | FAUJ880103 126 | FAUJ880104 127 | FAUJ880105 128 | FAUJ880106 129 | FAUJ880107 130 | FAUJ880108 131 | FAUJ880109 132 | FAUJ880110 133 | FAUJ880111 134 | FAUJ880112 135 | FAUJ880113 136 | FINA770101 137 | FINA910101 138 | FINA910102 139 | FINA910103 140 | FINA910104 141 | FODM020101 142 | FUKS010101 143 | FUKS010102 144 | FUKS010103 145 | FUKS010104 146 | FUKS010105 147 | FUKS010106 148 | FUKS010107 149 | FUKS010108 150 | FUKS010109 151 | FUKS010110 152 | FUKS010111 153 | FUKS010112 154 | GARJ730101 155 | GEIM800101 156 | GEIM800102 157 | GEIM800103 158 | GEIM800104 159 | GEIM800105 160 | GEIM800106 161 | GEIM800107 162 | GEIM800108 163 | GEIM800109 164 | GEIM800110 165 | GEIM800111 166 | GEOR030101 167 | GEOR030102 168 | GEOR030103 169 | GEOR030104 170 | GEOR030105 171 | GEOR030106 172 | GEOR030107 173 | GEOR030108 174 | GEOR030109 175 | GOLD730101 176 | GOLD730102 177 | GRAR740101 178 | GRAR740102 179 | GRAR740103 180 | GUOD860101 181 | GUYH850101 182 | GUYH850102 183 | GUYH850104 184 | GUYH850105 185 | HARY940101 186 | HOPA770101 187 | HOPT810101 188 | HUTJ700101 189 | HUTJ700102 190 | HUTJ700103 191 | ISOY800101 192 | ISOY800102 193 | ISOY800103 194 | ISOY800104 195 | ISOY800105 196 | ISOY800106 197 | ISOY800107 198 | ISOY800108 199 | JACR890101 200 | JANJ780101 201 | JANJ780102 202 | JANJ780103 203 | JANJ790101 204 | JANJ790102 205 | JOND750101 206 | JOND750102 207 | JOND920101 208 | JOND920102 209 | JUKT750101 210 | JUNJ780101 211 | JURD980101 212 | KANM800101 213 | KANM800102 214 | KANM800103 215 | KANM800104 216 | KARP850101 217 | KARP850102 218 | KARP850103 219 | KARS160101 220 | KARS160102 221 | KARS160103 222 | KARS160104 223 | KARS160105 224 | KARS160106 225 | KARS160107 226 | KARS160108 227 | KARS160109 228 | KARS160110 229 | KARS160111 230 | KARS160112 231 | KARS160113 232 | KARS160114 233 | KARS160115 234 | KARS160116 235 | KARS160117 236 | KARS160118 237 | KARS160119 238 | KARS160120 239 | KARS160121 240 | KARS160122 241 | KHAG800101 242 | KIDA850101 243 | KIMC930101 244 | KLEP840101 245 | KOEP990101 246 | KOEP990102 247 | KRIW710101 248 | KRIW790101 249 | KRIW790102 250 | KRIW790103 251 | KUHL950101 252 | KUMS000101 253 | KUMS000102 254 | KUMS000103 255 | KUMS000104 256 | KYTJ820101 257 | LAWE840101 258 | LEVM760101 259 | LEVM760102 260 | LEVM760103 261 | LEVM760104 262 | LEVM760105 263 | LEVM760106 264 | LEVM760107 265 | LEVM780101 266 | LEVM780102 267 | LEVM780103 268 | LEVM780104 269 | LEVM780105 270 | LEVM780106 271 | LEWP710101 272 | LIFS790101 273 | LIFS790102 274 | LIFS790103 275 | MANP780101 276 | MAXF760101 277 | MAXF760102 278 | MAXF760103 279 | MAXF760104 280 | MAXF760105 281 | MAXF760106 282 | MCMT640101 283 | MEEJ800101 284 | MEEJ800102 285 | MEEJ810101 286 | MEEJ810102 287 | MEIH800101 288 | MEIH800102 289 | MEIH800103 290 | MITS020101 291 | MIYS850101 292 | MIYS990101 293 | MIYS990102 294 | MIYS990103 295 | MIYS990104 296 | MIYS990105 297 | MONM990101 298 | MONM990201 299 | MUNV940101 300 | MUNV940102 301 | MUNV940103 302 | MUNV940104 303 | MUNV940105 304 | NADH010101 305 | NADH010102 306 | NADH010103 307 | NADH010104 308 | NADH010105 309 | NADH010106 310 | NADH010107 311 | NAGK730101 312 | NAGK730102 313 | NAGK730103 314 | NAKH900101 315 | NAKH900102 316 | NAKH900103 317 | NAKH900104 318 | NAKH900105 319 | NAKH900106 320 | NAKH900107 321 | NAKH900108 322 | NAKH900109 323 | NAKH900110 324 | NAKH900111 325 | NAKH900112 326 | NAKH900113 327 | NAKH920101 328 | NAKH920102 329 | NAKH920103 330 | NAKH920104 331 | NAKH920105 332 | NAKH920106 333 | NAKH920107 334 | NAKH920108 335 | NISK800101 336 | NISK860101 337 | NOZY710101 338 | OLSK800101 339 | ONEK900101 340 | ONEK900102 341 | OOBM770101 342 | OOBM770102 343 | OOBM770103 344 | OOBM770104 345 | OOBM770105 346 | OOBM850101 347 | OOBM850102 348 | OOBM850103 349 | OOBM850104 350 | OOBM850105 351 | PALJ810101 352 | PALJ810102 353 | PALJ810103 354 | PALJ810104 355 | PALJ810105 356 | PALJ810106 357 | PALJ810107 358 | PALJ810108 359 | PALJ810109 360 | PALJ810110 361 | PALJ810111 362 | PALJ810112 363 | PALJ810113 364 | PALJ810114 365 | PALJ810115 366 | PALJ810116 367 | PARJ860101 368 | PARS000101 369 | PARS000102 370 | PLIV810101 371 | PONJ960101 372 | PONP800101 373 | PONP800102 374 | PONP800103 375 | PONP800104 376 | PONP800105 377 | PONP800106 378 | PONP800107 379 | PONP800108 380 | PONP930101 381 | PRAM820101 382 | PRAM820102 383 | PRAM820103 384 | PRAM900101 385 | PRAM900102 386 | PRAM900103 387 | PRAM900104 388 | PTIO830101 389 | PTIO830102 390 | PUNT030101 391 | PUNT030102 392 | QIAN880101 393 | QIAN880102 394 | QIAN880103 395 | QIAN880104 396 | QIAN880105 397 | QIAN880106 398 | QIAN880107 399 | QIAN880108 400 | QIAN880109 401 | QIAN880110 402 | QIAN880111 403 | QIAN880112 404 | QIAN880113 405 | QIAN880114 406 | QIAN880115 407 | QIAN880116 408 | QIAN880117 409 | QIAN880118 410 | QIAN880119 411 | QIAN880120 412 | QIAN880121 413 | QIAN880122 414 | QIAN880123 415 | QIAN880124 416 | QIAN880125 417 | QIAN880126 418 | QIAN880127 419 | QIAN880128 420 | QIAN880129 421 | QIAN880130 422 | QIAN880131 423 | QIAN880132 424 | QIAN880133 425 | QIAN880134 426 | QIAN880135 427 | QIAN880136 428 | QIAN880137 429 | QIAN880138 430 | QIAN880139 431 | RACS770101 432 | RACS770102 433 | RACS770103 434 | RACS820101 435 | RACS820102 436 | RACS820103 437 | RACS820104 438 | RACS820105 439 | RACS820106 440 | RACS820107 441 | RACS820108 442 | RACS820109 443 | RACS820110 444 | RACS820111 445 | RACS820112 446 | RACS820113 447 | RACS820114 448 | RADA880101 449 | RADA880102 450 | RADA880103 451 | RADA880104 452 | RADA880105 453 | RADA880106 454 | RADA880107 455 | RADA880108 456 | RICJ880101 457 | RICJ880102 458 | RICJ880103 459 | RICJ880104 460 | RICJ880105 461 | RICJ880106 462 | RICJ880107 463 | RICJ880108 464 | RICJ880109 465 | RICJ880110 466 | RICJ880111 467 | RICJ880112 468 | RICJ880113 469 | RICJ880114 470 | RICJ880115 471 | RICJ880116 472 | RICJ880117 473 | ROBB760101 474 | ROBB760102 475 | ROBB760103 476 | ROBB760104 477 | ROBB760105 478 | ROBB760106 479 | ROBB760107 480 | ROBB760108 481 | ROBB760109 482 | ROBB760110 483 | ROBB760111 484 | ROBB760112 485 | ROBB760113 486 | ROBB790101 487 | ROSG850101 488 | ROSG850102 489 | ROSM880101 490 | ROSM880102 491 | ROSM880103 492 | SIMZ760101 493 | SNEP660101 494 | SNEP660102 495 | SNEP660103 496 | SNEP660104 497 | SUEM840101 498 | SUEM840102 499 | SUYM030101 500 | SWER830101 501 | TAKK010101 502 | TANS770101 503 | TANS770102 504 | TANS770103 505 | TANS770104 506 | TANS770105 507 | TANS770106 508 | TANS770107 509 | TANS770108 510 | TANS770109 511 | TANS770110 512 | TSAJ990101 513 | TSAJ990102 514 | VASM830101 515 | VASM830102 516 | VASM830103 517 | VELV850101 518 | VENT840101 519 | VHEG790101 520 | VINM940101 521 | VINM940102 522 | VINM940103 523 | VINM940104 524 | WARP780101 525 | WEBA780101 526 | WERD780101 527 | WERD780102 528 | WERD780103 529 | WERD780104 530 | WILM950101 531 | WILM950102 532 | WILM950103 533 | WILM950104 534 | WIMW960101 535 | WOEC730101 536 | WOLR790101 537 | WOLR810101 538 | WOLS870101 539 | WOLS870102 540 | WOLS870103 541 | YUTK870101 542 | YUTK870102 543 | YUTK870103 544 | YUTK870104 545 | ZASB820101 546 | ZHOH040101 547 | ZHOH040102 548 | ZHOH040103 549 | ZIMJ680101 550 | ZIMJ680102 551 | ZIMJ680103 552 | ZIMJ680104 553 | ZIMJ680105 -------------------------------------------------------------------------------- /Standalone/Data/aaindex.csv: -------------------------------------------------------------------------------- 1 | INDEX,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y 2 | ANDN920101,4.35,4.65,4.76,4.29,4.66,3.97,4.63,3.95,4.36,4.17,4.52,4.75,4.44,4.37,4.38,4.5,4.35,3.95,4.7,4.6 3 | ARGP820101,0.61,1.07,0.46,0.47,2.02,0.07,0.61,2.22,1.15,1.53,1.18,0.06,1.95,0,0.6,0.05,0.05,1.32,2.65,1.88 4 | ARGP820102,1.18,1.89,0.05,0.11,1.96,0.49,0.31,1.45,0.06,3.23,2.67,0.23,0.76,0.72,0.2,0.97,0.84,1.08,0.77,0.39 5 | ARGP820103,1.56,1.23,0.14,0.23,2.03,0.62,0.29,1.67,0.15,2.93,2.96,0.27,0.76,0.51,0.45,0.81,0.91,1.14,1.08,0.68 6 | AURR980101,0.94,0.6,1.19,1.41,1.06,1.18,1.15,1.07,1.03,0.95,0.88,0.79,1.18,0.94,1.15,0.69,0.87,0.9,0.91,1.04 7 | AURR980102,0.98,0.41,1.05,1.04,1.12,1.25,1.01,0.88,1.06,0.8,1.12,1.05,1.31,0.9,1.14,1.02,0.8,0.87,0.9,1.12 8 | AURR980103,1.05,0.6,1.39,1.11,0.95,1.26,1.43,0.95,0.97,0.96,0.99,0.91,1.05,0.87,0.81,0.96,1.03,0.62,1.06,0.94 9 | AURR980104,0.75,0.66,1.72,1.1,0.88,1.14,0.96,0.8,0.66,1.01,1.02,1.24,1.33,1.08,0.9,1.2,1.13,0.58,0.68,0.8 10 | AURR980105,0.67,0.37,1.58,0.94,0.96,0.98,0.83,0.78,0.84,0.79,0.98,1.28,1.12,1.05,0.76,1.25,1.41,0.67,0.94,0.82 11 | AURR980106,1.1,0.26,1.14,2.3,0.9,0.55,0.83,1.06,1.08,0.84,0.9,0.72,1.67,1.31,1.05,0.81,0.77,0.76,1.26,0.99 12 | AURR980107,1.39,0.52,1.64,2.07,1,0.65,1.36,0.64,0.8,0.91,1.1,0.67,0.94,1.6,0.95,0.69,0.92,0.7,1.1,0.73 13 | AURR980108,1.43,0.52,0.9,1.7,1.1,0.56,0.66,1.18,0.82,1.52,1.68,0.55,0.15,1.43,1.33,0.61,0.75,1.14,1.68,0.65 14 | AURR980109,1.55,0.59,0.61,1.34,1.39,0.37,0.89,1.47,1.27,1.36,2.13,0.6,0.03,1.43,1.39,0.44,0.65,1.18,1.1,0.93 15 | AURR980110,1.8,0.55,0.9,1.73,0.96,0.32,0.46,1.09,1.24,1.47,1.64,0.73,0.15,0.97,1.73,0.67,0.7,0.81,0.68,0.91 16 | AURR980111,1.52,0.26,1.04,1.76,1.14,0.3,0.83,1.25,1.1,1.26,1.14,0.58,0.44,1.41,1.49,0.66,0.73,1.03,0.68,1.04 17 | AURR980112,1.49,0.37,0.94,1.55,0.86,0.29,0.96,1.04,1.17,1.4,1.84,0.67,0.2,1.52,1.41,0.68,0.79,0.94,1.52,1.06 18 | AURR980113,1.73,0.63,0.68,1.16,1.35,0.32,0.76,1.15,1.22,1.8,2.21,0.7,0.07,0.88,1.24,0.65,0.46,0.94,1.57,1.1 19 | AURR980114,1.33,0.44,0.6,1.43,1.22,0.2,1.02,1.58,1.71,1.63,1.76,0.64,0.07,1.37,1.39,0.42,0.57,1.08,1,1.02 20 | AURR980115,1.87,0.33,0.91,1.88,0.67,0.33,0.89,0.9,1.63,1.65,1.35,0.7,0.03,1.24,1.66,0.71,0.5,0.51,1,0.73 21 | AURR980116,1.19,0.44,0.72,1.27,1.2,0.74,1.55,0.61,1.45,1.36,1.35,1.33,0.1,1.43,1.45,1.02,0.82,0.46,0.58,1.06 22 | AURR980117,0.77,0.44,0.79,0.92,1.04,2.74,1.65,0.64,1.19,0.66,0.74,1.39,0.66,0.95,1.11,0.64,0.82,0.53,0.58,0.93 23 | AURR980118,0.93,0.67,1.15,1.07,1.05,1.08,1.4,1.14,1.27,1.16,1.11,0.82,1.01,1.02,0.96,0.71,0.84,0.74,1.06,1.15 24 | AURR980119,1.09,0.26,1.17,1.31,0.84,0.97,0.88,0.97,1.13,0.87,0.96,1.03,2.01,1.08,1.29,0.76,0.79,0.77,0.91,0.64 25 | AURR980120,0.71,0.65,1.43,1.19,0.95,1.07,1.13,1.05,1.1,0.84,0.8,0.95,1.7,0.87,1.09,0.65,0.086,1.12,1.25,0.85 26 | BAEK050101,0.0166,0.5724,-0.1278,-0.1794,0.3561,-0.0442,0.1643,0.2758,-0.2134,0.2523,0.0197,-0.0786,-0.4188,-0.1051,-0.0762,-0.1629,-0.0701,0.1782,0.3836,0.25 27 | BASU050101,0.1366,0.2745,-0.1233,-0.0484,0.4076,-0.0464,0.0549,0.4172,-0.0101,0.4251,0.1747,-0.0345,0.0019,0.0325,0.0363,-0.0433,0.0589,0.4084,0.2362,0.3167 28 | BASU050102,0.0728,0.3557,-0.0552,-0.0295,0.4201,-0.0589,0.0874,0.3805,-0.0053,0.3819,0.1613,-0.039,-0.0492,0.0126,0.0394,-0.0282,0.0239,0.2947,0.4114,0.3113 29 | BASU050103,0.151,0.3222,0.0047,-0.0639,0.3455,0.0248,0.1335,0.4238,-0.0158,0.3926,0.216,0.0381,0.0844,0.0246,-0.0103,0.004,0.1462,0.3997,0.2657,0.2998 30 | BEGF750101,1,0.06,0.44,0.73,0.6,0.35,0.6,0.73,0.6,1,1,0.35,0.06,0.44,0.52,0.35,0.44,0.82,0.73,0.44 31 | BEGF750102,0.77,0.65,0.65,0.55,0.98,0.65,0.83,0.98,0.55,0.83,0.98,0.55,0.55,0.72,0.72,0.55,0.83,0.98,0.77,0.83 32 | BEGF750103,0.37,0.84,0.97,0.53,0.53,0.97,0.75,0.37,0.75,0.53,0.64,0.97,0.97,0.64,0.84,0.84,0.75,0.37,0.97,0.84 33 | BHAR880101,0.357,0.346,0.511,0.497,0.314,0.544,0.323,0.462,0.466,0.365,0.295,0.463,0.509,0.493,0.529,0.507,0.444,0.386,0.305,0.42 34 | BIGC670101,52.6,68.3,68.4,84.7,113.9,36.3,91.9,102,105.1,102,97.7,75.7,73.6,89.7,109.1,54.9,71.2,85.1,135.4,116.2 35 | BIOV880101,16,168,-78,-106,189,-13,50,151,-141,145,124,-74,-20,-73,-70,-70,-38,123,145,53 36 | BIOV880102,44,90,-91,-139,148,-8,47,100,-188,108,121,-72,-36,-117,-68,-60,-54,117,163,22 37 | BLAM930101,0.96,0.42,0.42,0.53,0.59,0,0.57,0.84,0.73,0.92,0.86,0.39,-2.5,0.8,0.77,0.53,0.54,0.63,0.58,0.72 38 | BLAS910101,0.616,0.68,0.028,0.043,1,0.501,0.165,0.943,0.283,0.943,0.738,0.236,0.711,0.251,0,0.359,0.45,0.825,0.878,0.88 39 | BROC820101,7.3,-9.2,-2.9,-7.1,19.2,-1.2,-2.1,6.6,-3.7,20,5.6,-5.7,5.1,-0.3,-3.6,-4.1,0.8,3.5,16.3,5.9 40 | BROC820102,3.9,-14.3,-2.8,-7.5,14.7,-2.3,2,11,-2.5,15,4.1,-2.8,5.6,1.8,3.2,-3.5,1.1,2.1,17.8,3.8 41 | BULH740101,-0.2,-0.45,-0.2,-0.3,-2.33,0,-0.12,-2.26,-0.35,-2.46,-1.47,0.08,-0.98,0.16,-0.12,-0.39,-0.52,-1.56,-2.01,-2.24 42 | BULH740102,0.691,0.624,0.558,0.632,0.756,0.592,0.646,0.809,0.767,0.842,0.709,0.596,0.73,0.649,0.728,0.594,0.655,0.777,0.743,0.743 43 | BUNA790101,8.249,8.312,8.41,8.368,8.228,8.391,8.415,8.195,8.408,8.423,8.418,8.747,0,8.411,8.274,8.38,8.236,8.436,8.094,8.183 44 | BUNA790102,4.349,4.686,4.765,4.295,4.663,3.972,4.63,4.224,4.358,4.385,4.513,4.755,4.471,4.373,4.396,4.498,4.346,4.184,4.702,4.604 45 | BUNA790103,6.5,7.7,7,7,9.4,5.6,8,7,6.5,6.5,0,7.5,0,6,6.9,6.5,6.9,7,0,6.8 46 | BURA740101,0.486,0.2,0.288,0.538,0.318,0.12,0.4,0.37,0.402,0.42,0.417,0.193,0.208,0.418,0.262,0.2,0.272,0.379,0.462,0.161 47 | BURA740102,0.288,0.533,0.271,0.262,0.318,0.312,0.2,0.411,0.265,0.4,0.375,0.229,0.34,0.327,0.362,0.354,0.388,0.495,0.231,0.429 48 | CASG920101,0.2,1.9,-1.4,-1.3,1,-0.1,0.4,1.4,-1.6,0.5,0.5,-0.5,-1,-1.1,-0.7,-0.7,-0.4,0.7,1.6,0.5 49 | CEDJ970101,8.6,2.9,4.9,5.1,3.7,7.8,2.1,4.6,6.3,8.8,2.5,4.6,4.9,4,4.2,7.3,6,6.7,1.4,3.6 50 | CEDJ970102,7.6,2.2,5.2,6.2,4,6.9,2.1,5.1,5.8,9.4,2.1,4.4,5.4,4.1,5,7.2,6.1,6.7,1.4,3.2 51 | CEDJ970103,8.1,2,3.8,4.6,5.6,7,2,6.7,4.4,11,2.8,3.7,4.7,3.1,4.6,7.3,5.6,7.7,1.8,3.3 52 | CEDJ970104,7.9,1.9,5.5,7.1,3.9,7.1,2.1,5.2,6.7,8.6,2.4,4,5.3,4.4,4.9,6.6,5.3,6.8,1.2,3.1 53 | CEDJ970105,8.3,1.6,4.7,6.5,2.7,6.3,2.1,3.7,7.9,7.4,2.3,3.7,6.9,4.7,8.7,8.8,5.1,5.3,0.7,2.4 54 | CHAM810101,0.52,0.62,0.76,0.68,0.7,0,0.7,1.02,0.68,0.98,0.78,0.76,0.36,0.68,0.68,0.53,0.5,0.76,0.7,0.7 55 | CHAM820101,0.046,0.128,0.105,0.151,0.29,0,0.23,0.186,0.219,0.186,0.221,0.134,0.131,0.18,0.291,0.062,0.108,0.14,0.409,0.298 56 | CHAM820102,-0.368,4.53,2.06,1.77,1.06,-0.525,0,0.791,0,1.07,0.656,0,-2.24,0.731,-1.03,-0.524,0,0.401,1.6,4.91 57 | CHAM830101,0.71,1.19,1.21,0.84,0.71,1.52,1.07,0.66,0.99,0.69,0.59,1.37,1.61,0.87,1.06,1.34,1.08,0.63,0.76,1.07 58 | CHAM830102,-0.118,0.083,0.048,-0.245,0.015,0.104,0.138,0.23,0.032,-0.052,-0.258,0.289,0,-0.105,0.124,0.225,0.166,0.513,0.158,0.094 59 | CHAM830103,0,1,1,1,1,0,1,2,1,1,1,1,0,1,1,1,2,2,1,1 60 | CHAM830104,0,0,1,1,1,0,1,1,1,2,1,1,0,1,1,0,0,0,1,1 61 | CHAM830105,0,0,0,1,1,0,1,0,1,0,1,0,0,1,1,0,0,0,1.5,1 62 | CHAM830106,0,1,2,3,4,0,3,2,4,2,3,2,0,3,5,1,1,1,5,5 63 | CHAM830107,0,0,1,1,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0 64 | CHAM830108,0,1,0,0,1,0,1,0,1,0,1,1,0,1,1,0,0,0,1,1 65 | CHOC750101,91.5,117.7,124.5,155.1,203.4,66.4,167.3,168.8,171.3,167.9,170.8,135.2,129.3,161.1,202,99.1,122.1,141.7,237.6,203.6 66 | CHOC760101,115,135,150,190,210,75,195,175,200,170,185,160,145,180,225,115,140,155,255,230 67 | CHOC760102,25,19,50,49,24,23,43,18,97,23,31,63,50,71,90,44,47,18,32,60 68 | CHOC760103,0.38,0.45,0.15,0.18,0.5,0.36,0.17,0.6,0.03,0.45,0.4,0.12,0.18,0.07,0.01,0.22,0.23,0.54,0.27,0.15 69 | CHOC760104,0.2,0.22,0.04,0.03,0.14,0.18,0.02,0.19,0,0.16,0.11,0.03,0.04,0.01,0,0.08,0.08,0.18,0.04,0.03 70 | CHOP780101,0.66,1.19,1.46,0.74,0.6,1.56,0.95,0.47,1.01,0.59,0.6,1.56,1.52,0.98,0.95,1.43,0.96,0.5,0.96,1.14 71 | CHOP780201,1.42,0.7,1.01,1.51,1.13,0.57,1,1.08,1.16,1.21,1.45,0.67,0.57,1.11,0.98,0.77,0.83,1.06,1.08,0.69 72 | CHOP780202,0.83,1.19,0.54,0.37,1.38,0.75,0.87,1.6,0.74,1.3,1.05,0.89,0.55,1.1,0.93,0.75,1.19,1.7,1.37,1.47 73 | CHOP780203,0.74,0.96,1.52,0.95,0.66,1.56,0.95,0.47,1.19,0.5,0.6,1.46,1.56,0.96,1.01,1.43,0.98,0.59,0.6,1.14 74 | CHOP780204,1.29,0.66,2.02,2.44,0.61,0.76,0.73,0.67,0.66,0.58,0.71,0.81,2.01,1.22,0.44,0.74,1.08,0.61,1.47,0.68 75 | CHOP780205,1.2,1.11,0.61,1.24,1.1,0.42,1.77,0.98,1.83,1.13,1.57,0.59,0,1.22,1.25,0.96,0.75,1.25,0.4,0.73 76 | CHOP780206,0.7,0.65,0.98,1.04,0.93,1.41,1.22,0.78,1.01,0.85,0.83,1.42,1.1,0.75,0.34,1.55,1.09,0.75,0.62,0.99 77 | CHOP780207,0.52,0.94,1.06,0.59,1.04,1.64,1.86,0.87,1.49,0.84,0.52,1.64,1.58,0.7,1.24,0.93,0.86,0.32,0.16,0.96 78 | CHOP780208,0.86,0.87,0.38,0.35,1.5,0.63,0.54,1.94,1,1.3,1.43,0.66,0.66,1.65,0.9,0.63,1.17,1.69,1.49,1.07 79 | CHOP780209,0.75,1.11,0.85,0.55,1.5,0.74,0.9,1.35,0.74,1.27,0.95,1.21,0.4,0.65,0.9,0.79,0.75,1.79,1.19,1.96 80 | CHOP780210,0.67,1.34,1.39,0.92,0.3,1.46,0.78,0.59,1.09,0.46,0.52,1.86,1.58,1.09,0.89,1.41,1.09,0.42,0.48,1.23 81 | CHOP780211,0.74,0.53,1.32,0.85,0.44,1.68,0.96,0.53,0.82,0.59,0.85,1.13,1.69,0.77,1.05,1.49,1.16,0.59,1.59,1.01 82 | CHOP780212,0.06,0.149,0.147,0.056,0.059,0.102,0.14,0.043,0.055,0.061,0.068,0.161,0.102,0.074,0.07,0.12,0.086,0.062,0.077,0.082 83 | CHOP780213,0.076,0.053,0.11,0.06,0.041,0.085,0.047,0.034,0.115,0.025,0.082,0.083,0.301,0.098,0.106,0.139,0.108,0.048,0.013,0.065 84 | CHOP780214,0.035,0.117,0.179,0.077,0.065,0.19,0.093,0.013,0.072,0.036,0.014,0.191,0.034,0.037,0.099,0.125,0.065,0.028,0.064,0.114 85 | CHOP780215,0.058,0.128,0.081,0.064,0.065,0.152,0.054,0.056,0.095,0.07,0.055,0.091,0.068,0.098,0.085,0.106,0.079,0.053,0.167,0.125 86 | CHOP780216,0.64,0.92,1.61,0.8,0.62,1.63,0.77,0.29,1.13,0.36,0.51,1.56,2.04,0.84,1.05,1.52,0.98,0.43,0.48,1.08 87 | CIDH920101,-0.45,0.79,-1.52,-0.8,1.48,-1,1.07,0.76,-0.36,1.29,1.37,-0.2,-0.12,-0.99,-0.24,-0.98,-0.7,1.26,1.38,1.49 88 | CIDH920102,-0.08,0.76,-0.71,-1.31,1.53,-0.84,0.43,1.39,-0.09,1.24,1.27,-0.7,-0.01,-0.4,-0.09,-0.93,-0.59,1.09,2.25,1.53 89 | CIDH920103,0.36,0.7,-1.09,-0.83,1.01,-0.82,0.16,2.17,-0.56,1.18,1.21,-0.9,-0.06,-1.05,-0.52,-0.6,-1.2,1.21,1.31,1.05 90 | CIDH920104,0.17,1.24,-1.05,-1.19,1.29,-0.57,-0.25,2.06,-0.62,0.96,0.6,-0.9,-0.21,-1.2,-0.7,-0.83,-0.62,1.21,1.51,0.66 91 | CIDH920105,0.02,0.77,-1.04,-1.14,1.35,-0.8,0.26,1.81,-0.41,1.14,1,-0.77,-0.09,-1.1,-0.42,-0.97,-0.77,1.13,1.71,1.11 92 | COHE430101,0.75,0.61,0.6,0.66,0.77,0.64,0.67,0.9,0.82,0.9,0.75,0.61,0.76,0.67,0.7,0.68,0.7,0.86,0.74,0.71 93 | CORJ870101,50.76,58.74,43.17,43.48,53.45,50.27,49.33,57.3,42.92,53.89,52.75,45.8,45.39,46.09,48.66,47.24,49.26,56.12,53.59,51.79 94 | CORJ870102,-0.414,0.162,-1.31,-1.218,1.938,-0.684,-0.63,1.237,-0.67,1.215,1.02,-0.916,-0.503,-0.905,-0.584,-0.563,-0.289,0.899,0.514,1.699 95 | CORJ870103,-0.96,4.54,-5.68,-3.86,5.06,-1.28,-0.62,5.54,-5.62,6.81,4.76,-1.94,-4.47,-5.3,0.75,-1.92,-3.99,5.39,0.21,3.34 96 | CORJ870104,-0.26,0.83,-1.3,-0.73,1.09,-0.4,-0.18,1.1,-1.01,1.52,1.09,-0.46,-0.62,-0.83,0.08,-0.55,-0.71,1.15,-0.13,0.69 97 | CORJ870105,-0.73,0.64,-6.13,-2.9,5.2,-2.67,3.03,5.04,-5.99,4.91,3.34,-5.29,-4.32,-0.96,-1.03,-3,-1.91,3.98,0.51,2.87 98 | CORJ870106,-1.35,4.37,-11.88,-4.56,11.35,-5.82,6.54,10.93,-11.92,9.88,7.47,-10.96,-10.86,-1.34,-3.89,-6.21,-4.83,8.2,1.8,7.61 99 | CORJ870107,-0.56,1.78,-4.31,-2.35,3.67,-1.35,0.81,3.83,-4.08,4.09,3.11,-2.87,-3.22,-2.31,-0.26,-1.85,-1.97,3.31,-0.11,2.17 100 | CORJ870108,1.37,-4.47,8.93,4.04,-7.96,3.39,-1.65,-7.92,7.7,-8.68,-7.13,6.29,6.25,3.88,1.33,4.08,4.02,-6.94,0.79,-4.73 101 | COSI940101,0.0373,0.0829,0.1263,0.0058,0.0946,0.005,0.0242,0,0.0371,0,0.0823,0.0036,0.0198,0.0761,0.0959,0.0829,0.0941,0.0057,0.0548,0.0516 102 | COWR900101,0.42,0.84,-0.51,-0.37,1.74,0,-2.28,1.81,-2.03,1.8,1.18,-1.03,0.86,-0.96,-1.56,-0.64,-0.26,1.34,1.46,0.51 103 | CRAJ730101,1.33,0.93,0.97,1.66,1.15,0.58,1.49,0.99,1.03,1.29,1.4,0.72,0.49,1.42,0.79,0.83,0.94,0.96,1.33,0.49 104 | CRAJ730102,1,0.99,0.89,0.37,1.26,0.56,0.36,1.75,1.18,1.53,1.4,0.75,0.36,0.87,0.74,0.65,1.15,1.61,0.84,1.41 105 | CRAJ730103,0.6,1.29,1.24,0.64,1.05,1.38,0.95,0.67,1.1,0.7,0.67,1.42,1.47,0.92,0.79,1.26,1.05,0.48,1.23,1.35 106 | DAWD720101,2.5,3,2.5,5,6.5,0.5,6,5.5,7,5.5,6,5,5.5,6,7.5,3,5,5,7,7 107 | DAYM780101,8.6,2.9,5.5,6,3.6,8.4,2,4.5,6.6,7.4,1.7,4.3,5.2,3.9,4.9,7,6.1,6.6,1.3,3.4 108 | DAYM780201,100,20,106,102,41,49,66,96,56,40,94,134,56,93,65,120,97,74,18,41 109 | DESM900101,1.56,1.8,0.23,0.19,1.42,1.03,1,1.27,0.15,1.38,1.93,0.51,0.27,0.39,0.59,0.96,1.11,1.58,0.91,1.1 110 | DESM900102,1.26,1.6,0.27,0.23,1.46,1.08,1,1.44,0.33,1.36,1.52,0.59,0.54,0.39,0.38,0.98,1.01,1.33,1.06,0.89 111 | DIGM050101,1.076,0.753,1.29,1.118,0.869,1.346,0.985,0.926,1.105,1.054,0.974,1.056,0.82,0.729,1.361,1.342,0.871,1.131,0.666,0.531 112 | EISD840101,0.25,0.04,-0.72,-0.62,0.61,0.16,-0.4,0.73,-1.1,0.53,0.26,-0.64,-0.07,-0.69,-1.76,-0.26,-0.18,0.54,0.37,0.02 113 | EISD860101,0.67,0.38,-1.2,-0.76,2.3,0,0.64,1.9,-0.57,1.9,2.4,-0.6,1.2,-0.22,-2.1,0.01,0.52,1.5,2.6,1.6 114 | EISD860102,0,0.17,1.9,3,1.1,0,0.99,1.2,5.7,1,1.9,1.3,0.18,1.9,10,0.73,1.5,0.48,1.6,1.8 115 | EISD860103,0,0.76,-0.98,-0.89,0.92,0,-0.75,0.99,-0.99,0.89,0.94,-0.86,0.22,-1,-0.96,-0.67,0.09,0.84,0.67,-0.93 116 | 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FAUJ880101,1.28,1.77,1.6,1.56,2.94,0,2.99,4.19,1.89,2.59,2.35,1.6,2.67,1.56,2.34,1.31,3.03,3.67,3.21,2.94 125 | FAUJ880102,0.53,0.66,0.59,0.72,0.71,0,0.64,0.96,0.78,0.92,0.77,0.58,0,0.71,0.69,0.55,0.63,0.89,0.84,0.71 126 | FAUJ880103,1,2.43,2.78,3.78,5.89,0,4.66,4,4.77,4,4.43,2.95,2.72,3.95,6.13,1.6,2.6,3,8.08,6.47 127 | FAUJ880104,2.87,4.47,4.74,5.97,4.62,2.06,5.23,4.92,6.89,4.92,6.36,4.58,4.11,6.11,7.82,3.97,4.11,4.11,7.68,4.73 128 | FAUJ880105,1.52,1.52,1.52,1.52,1.52,1,1.52,1.9,1.52,1.52,1.52,1.52,1.52,1.52,1.52,1.52,1.73,1.9,1.52,1.52 129 | FAUJ880106,2.04,3.41,3.78,3.31,6.02,1,5.66,3.49,4.87,4.45,4.8,4.37,4.31,3.53,6.24,2.7,3.17,3.17,5.9,6.72 130 | FAUJ880107,7.3,14.4,9.2,11.4,13.9,0,10.2,16.1,10.9,10.1,10.4,8,17.8,10.6,11.1,13.1,16.7,17.2,13.2,13.9 131 | FAUJ880108,-0.01,0.12,0.15,0.07,0.03,0,0.08,-0.01,0,-0.01,0.04,0.06,0,0.05,0.04,0.11,0.04,0.01,0,0.03 132 | FAUJ880109,0,0,1,1,0,0,1,0,2,0,0,2,0,2,4,1,1,0,1,1 133 | FAUJ880110,0,0,4,4,0,0,1,0,1,0,0,3,0,3,3,2,2,0,0,2 134 | FAUJ880111,0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,0,0,0,0 135 | FAUJ880112,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 136 | FAUJ880113,4.76,3.67,5.69,5.48,4.31,3.77,2.84,4.81,4.27,4.79,4.25,3.64,0,4.54,4.3,3.83,3.87,4.86,4.75,4.3 137 | FINA770101,1.08,0.95,0.85,1.15,1.1,0.55,1,1.05,1.15,1.25,1.15,0.85,0.71,0.95,1.05,0.75,0.75,0.95,1.1,1.1 138 | FINA910101,1,1,3.2,1.7,1,1,1,0.6,0.7,1,1,1.7,1,1,0.7,1.7,1.7,0.6,1,1 139 | FINA910102,1,1,1.7,1.7,1,1.3,1,1,0.7,1,1,1,13,1,0.7,1,1,1,1,1 140 | FINA910103,1.2,1,0.7,0.7,1,0.8,1.2,0.8,1.7,1,1,1.2,1,1,1.7,1.5,1,0.8,1,1 141 | FINA910104,1,1,0.7,0.7,1,1.5,1,1,1.7,1,1,1,0.1,1,1.7,1,1,1,1,1 142 | FODM020101,0.7,1.17,0.87,0.96,1.34,0.64,1.39,1.29,0.91,1.44,0.91,1.47,0.12,0.73,0.95,0.84,0.74,1.2,1.8,1.68 143 | FUKS010101,4.47,0.29,7.05,16.56,2.32,8.29,1.74,3.3,12.98,5.06,1.71,3.89,5.41,2.87,8.48,4.27,3.83,4.05,0.67,2.75 144 | FUKS010102,6.77,0.31,8.57,12.93,1.92,7.95,2.8,2.72,10.2,4.43,1.87,5.5,4.79,5.24,6.87,5.41,5.36,3.57,0.54,2.26 145 | FUKS010103,7.43,0.42,8.71,5.86,1.18,9.4,1.49,1.76,9.67,2.74,0.6,9.12,5.6,5.42,4.51,9.6,8.95,3.1,1.18,3.26 146 | FUKS010104,5.22,1.01,7.91,10.66,1.68,5.81,2.27,2.36,12.68,4.52,1.85,6.06,5.7,6,7.3,6.99,5.16,4.1,0.56,2.16 147 | FUKS010105,9.88,1.12,3.5,4.02,5.27,6.88,1.88,10.08,3.39,13.21,2.44,2.35,3.8,1.66,3.71,4.1,4.98,12.53,1.11,4.07 148 | FUKS010106,10.98,1.47,3.37,3.51,4.97,7.48,2.2,9.74,2.54,12.79,3.1,2.85,3.42,2.3,3.26,4.93,5.55,10.69,1.28,3.55 149 | FUKS010107,9.95,1.3,4.46,2.58,5.41,8.87,1.99,7.73,2,9.66,2.45,4.84,3.2,2.64,3.05,6.03,5.62,9.46,2.6,6.15 150 | FUKS010108,8.26,2.67,2.8,2.67,7.32,5.62,1.98,8.95,1.89,16.46,2.67,2.54,3.3,2.86,2.8,6,5,10.24,2.01,3.96 151 | FUKS010109,7.39,0.74,5.14,9.8,3.91,7.53,1.82,6.96,7.81,9.45,2.1,3.06,4.54,2.22,5.91,4.18,4.45,8.62,0.9,3.46 152 | FUKS010110,9.07,0.95,5.73,7.77,3.59,7.69,2.47,6.56,6.01,9,2.54,4.05,4.04,3.63,4.9,5.15,5.46,7.47,0.95,2.96 153 | FUKS010111,8.82,0.9,6.38,4.05,3.51,9.11,1.77,5.05,5.45,6.54,1.62,6.77,4.28,3.89,3.71,7.64,7.12,6.6,1.96,4.85 154 | FUKS010112,6.65,1.79,5.5,6.89,4.34,5.72,2.13,5.47,7.59,10.15,2.24,4.4,4.56,4.52,5.17,6.52,5.08,7,1.24,3.01 155 | GARJ730101,0.28,0.28,0.21,0.33,2.18,0.17,0.21,0.82,0.09,1,0.74,0.25,0.39,0.35,0.1,0.12,0.21,0.6,5.7,1.26 156 | GEIM800101,1.29,0.79,1.1,1.49,1.13,0.63,1.33,1.05,1.33,1.31,1.54,0.81,0.63,1.07,1,0.78,0.77,0.81,1.18,0.71 157 | GEIM800102,1.13,1.32,0.94,1.2,1.01,0.83,1.09,1.05,1.08,1.13,1.23,1.06,0.82,0.93,1.09,1.01,1.17,1.13,1.32,0.88 158 | GEIM800103,1.55,1.44,1.55,1.67,0.4,0.59,1.21,1.27,1.2,1.25,1.37,1.2,0.21,1.13,0.2,1.01,0.55,0.64,1.86,1.08 159 | GEIM800104,1.19,0.95,1.07,1.64,1.02,0.6,1.03,1.12,1.27,1.18,1.49,0.94,0.68,1.32,1,0.81,0.85,0.74,1.18,0.77 160 | GEIM800105,0.84,1.27,0.59,0.57,1.15,0.94,0.81,1.29,0.86,1.1,0.88,0.66,0.8,1.02,1.04,1.05,1.2,1.56,1.15,1.39 161 | GEIM800106,0.86,0.91,0.66,0.37,1.34,0.86,1.07,1.17,1.01,1.28,1.15,0.6,0.61,1.11,1.15,0.91,1.14,1.31,1.13,1.37 162 | GEIM800107,0.91,1.12,0.74,0.41,1.26,0.91,1.01,1.29,0.86,1.23,0.96,0.72,0.65,0.9,0.99,0.93,1.05,1.58,1.15,1.21 163 | GEIM800108,0.91,0.93,1.4,0.97,0.72,1.51,0.9,0.65,0.82,0.59,0.58,1.64,1.66,0.94,1,1.23,1.04,0.6,0.67,0.92 164 | GEIM800109,0.8,0,1.6,0.4,1.2,2,0.96,0.85,0.94,0.8,0.39,1.1,2.1,1.6,0.96,1.3,0.6,0.8,0,1.8 165 | GEIM800110,1.1,1.05,1.41,1.4,0.6,1.3,0.85,0.67,0.94,0.52,0.69,1.57,1.77,0.81,0.93,1.13,0.88,0.58,0.62,0.41 166 | GEIM800111,0.93,0.92,1.22,1.05,0.71,1.45,0.96,0.58,0.91,0.59,0.6,1.36,1.67,0.83,1.01,1.25,1.08,0.62,0.68,0.98 167 | GEOR030101,0.964,0.778,0.916,1.051,1.119,0.835,1.014,0.922,0.944,1.085,1.032,0.944,1.299,1.047,1.143,0.947,1.017,0.955,0.895,1 168 | GEOR030102,0.974,0.972,0.892,1.054,1.122,0.845,0.949,0.928,0.946,1.11,0.923,0.988,1.362,1.092,1.129,0.932,1.023,0.923,0.879,0.902 169 | GEOR030103,0.938,0.6856,0.857,1.139,1.11,0.892,1.109,0.986,0.952,1,1.077,0.902,1.266,0.916,1.137,0.956,1.018,0.959,0.971,1.157 170 | GEOR030104,1.042,0.5,0.97,0.992,0.981,0.743,1.034,0.852,0.979,1.193,0.998,0.828,1.332,1.111,1.069,0.984,0.992,1.001,0.96,1.12 171 | GEOR030105,1.065,1.015,0.836,0.736,1.368,1.022,0.973,1.189,0.478,1.192,1.369,0.762,1.241,0.861,1.131,1.097,0.822,1.14,1.017,0.836 172 | GEOR030106,0.99,0.644,0.915,1.053,1.121,0.785,1.054,0.95,1.003,1.106,1.093,0.873,1.314,0.999,1.132,0.911,0.988,0.957,0.939,1.09 173 | GEOR030107,0.892,1.035,0.925,1.115,1.058,0.917,0.992,0.817,0.944,0.994,0.782,1.144,1.309,1.2,1.154,0.986,1.11,0.9,0.841,0.866 174 | GEOR030108,1.092,0.662,0.919,1.199,1.09,0.698,1.012,0.912,1.008,1.276,1.171,0.927,0.8,1.124,1.239,0.886,0.832,0.908,0.981,1.075 175 | GEOR030109,0.843,0.896,0.906,0.9,1.151,0.978,1.05,0.946,0.893,0.885,0.878,0.956,1.816,0.968,1.038,1.003,1.189,0.999,0.852,0.945 176 | GOLD730101,0.75,1,0,0,2.65,0,0,2.95,1.5,2.4,1.3,0.69,2.6,0.59,0.75,0,0.45,1.7,3,2.85 177 | GOLD730102,88.3,112.4,110.8,140.5,189,60,152.6,168.5,175.6,168.5,162.2,125.1,122.2,148.7,181.2,88.7,118.2,141.4,227,193 178 | GRAR740101,0,2.75,1.38,0.92,0,0.74,0.58,0,0.33,0,0,1.33,0.39,0.89,0.65,1.42,0.71,0,0.13,0.2 179 | GRAR740102,8.1,5.5,13,12.3,5.2,9,10.4,5.2,11.3,4.9,5.7,11.6,8,10.5,10.5,9.2,8.6,5.9,5.4,6.2 180 | GRAR740103,31,55,54,83,132,3,96,111,119,111,105,56,32.5,85,124,32,61,84,170,136 181 | GUOD860101,25,32,2,14,100,-2,-26,91,-26,100,68,-7,25,0,-7,-2,7,62,109,56 182 | GUYH850101,0.1,-1.42,0.78,0.83,-2.12,0.33,-0.5,-1.13,1.4,-1.18,-1.59,0.48,0.73,0.95,1.91,0.52,0.07,-1.27,-0.51,-0.21 183 | GUYH850102,0.05,-0.84,0.41,0.38,-0.45,0.31,-0.41,-0.69,0.57,-0.62,-0.38,0.29,0.46,0.46,0.12,0.12,0.38,-0.46,-0.98,-0.25 184 | GUYH850104,-0.31,-0.87,0.58,0.68,-0.45,-0.33,0.13,-0.66,1.79,-0.53,-0.38,0.49,0.34,0.7,1.3,0.1,0.21,-0.62,-0.27,0.4 185 | GUYH850105,-0.27,-0.23,0.5,0.33,-0.55,-0.22,0.37,-0.8,1.17,-0.44,-0.31,0.61,0.36,1,2,0.17,0.18,-0.65,0.05,0.48 186 | HARY940101,90.1,113.2,117.1,140.8,193.5,63.8,159.3,164.9,170,164.6,167.7,127.5,123.1,149.4,192.8,94.2,120,139.1,197.1,231.7 187 | HOPA770101,1,0.1,6.5,6.2,1.4,1.1,2.8,0.8,5.3,0.8,0.7,2.2,0.9,2.1,2.3,1.7,1.5,0.9,1.9,2.1 188 | HOPT810101,-0.5,-1,3,3,-2.5,0,-0.5,-1.8,3,-1.8,-1.3,0.2,0,0.2,3,0.3,-0.4,-1.5,-3.4,-2.3 189 | HUTJ700101,29.22,50.7,37.09,41.84,48.52,23.71,59.64,45,57.1,48.03,69.32,38.3,36.13,44.02,26.37,32.4,35.2,40.35,56.92,51.73 190 | HUTJ700102,30.88,53.83,40.66,44.98,51.06,24.74,65.99,49.71,63.21,50.62,55.32,41.7,39.21,46.62,68.43,35.65,36.5,42.75,60,51.15 191 | HUTJ700103,154.33,219.79,194.91,223.16,204.74,127.9,242.54,233.21,300.46,232.3,202.65,207.9,179.93,235.51,341.01,174.06,205.8,207.6,237.01,229.15 192 | ISOY800101,1.53,0.89,1,1.63,1.22,0.44,1.03,1.07,1.26,1.32,1.66,0.6,0.25,1.27,1.17,0.65,0.86,0.93,1.05,0.7 193 | ISOY800102,0.86,1.39,0.69,0.66,1.16,0.7,1.06,1.31,0.77,1.01,1.06,0.74,1.16,0.89,0.98,1.09,1.24,1.4,1.17,1.28 194 | ISOY800103,0.78,0.6,1.5,0.97,0.67,1.73,0.83,0.4,1.01,0.57,0.3,1.56,1.55,0.78,1.06,1.19,1.09,0.44,0.74,1.14 195 | ISOY800104,1.09,0.5,0.77,0.92,0.5,1.25,0.67,0.66,1.25,0.44,0.45,1.14,2.96,0.83,0.97,1.21,1.33,0.56,0.62,0.94 196 | ISOY800105,0.35,0.5,2.16,0.65,0.89,2.4,1.19,0.12,0.83,0.58,0.22,2.12,0.43,0.73,0.75,1.24,0.85,0.43,0.62,1.44 197 | ISOY800106,1.09,1.04,1.24,1.14,0.8,0.27,1.07,0.97,1.2,1.3,0.55,0.88,1.78,1.09,1.07,1.2,0.99,0.77,1.03,0.69 198 | ISOY800107,1.34,1.44,1.77,2.54,0.43,0.95,0,0.52,0.79,1.05,0,0.92,0.37,0.79,2.78,0.87,1.14,0,1.79,0.73 199 | ISOY800108,0.47,0.41,1.15,0.64,0.61,3.03,0.89,0.62,0.98,0.53,0.68,2.16,0.63,0.95,0.52,1.03,0.39,0.76,0.63,0.83 200 | JACR890101,0.18,0.27,-2.36,-2.1,0.5,0.09,-1.48,0.37,-2.53,0.41,0.44,-1.3,-0.2,-1.22,-5.4,-0.4,-0.34,0.32,-0.01,-0.08 201 | JANJ780101,27.8,15.5,60.6,68.2,25.5,24.5,50.7,22.8,103,27.6,33.5,60.1,51.5,68.7,94.7,42,45,23.7,34.7,55.2 202 | JANJ780102,51,74,19,16,58,52,34,66,3,60,52,22,25,16,5,35,30,64,49,24 203 | JANJ780103,15,5,50,55,10,10,34,13,85,16,20,49,45,56,67,32,32,14,17,41 204 | JANJ790101,1.7,4.6,0.4,0.3,2.2,1.8,0.8,3.1,0.05,2.4,1.9,0.4,0.6,0.3,0.1,0.8,0.7,2.9,1.6,0.5 205 | JANJ790102,0.3,0.9,-0.6,-0.7,0.5,0.3,-0.1,0.7,-1.8,0.5,0.4,-0.5,-0.3,-0.7,-1.4,-0.1,-0.2,0.6,0.3,-0.4 206 | JOND750101,0.87,1.52,0.66,0.67,2.87,0.1,0.87,3.15,1.64,2.17,1.67,0.09,2.77,0,0.85,0.07,0.07,1.87,3.77,2.67 207 | JOND750102,2.34,1.65,2.01,2.19,1.83,2.34,1.82,2.36,2.18,2.36,2.28,2.02,1.99,2.17,1.18,2.21,2.1,2.32,2.38,2.2 208 | JOND920101,0.077,0.02,0.052,0.062,0.04,0.074,0.023,0.053,0.059,0.091,0.024,0.043,0.051,0.041,0.051,0.069,0.059,0.066,0.014,0.032 209 | JOND920102,100,44,86,77,51,50,91,103,72,54,93,104,58,84,83,117,107,98,25,50 210 | JUKT750101,5.3,1.3,3.6,3.3,2.3,4.8,1.4,3.1,4.1,4.7,1.1,3,2.5,2.4,2.6,4.5,3.7,4.2,0.8,2.3 211 | JUNJ780101,685,241,400,427,303,707,155,394,575,581,132,397,366,313,382,593,490,553,99,292 212 | JURD980101,1.1,2.5,-3.6,-3.2,2.8,-0.64,-3.2,4.5,-4.11,3.8,1.9,-3.5,-1.9,-3.68,-5.1,-0.5,-0.7,4.2,-0.46,-1.3 213 | KANM800101,1.36,0.82,1.04,1.48,1.05,0.63,1.11,1.08,1.22,1.21,1.45,0.89,0.52,1.14,1,0.74,0.81,0.94,0.97,0.79 214 | KANM800102,0.81,1.17,0.71,0.53,1.2,0.88,0.92,1.48,0.77,1.24,1.05,0.62,0.61,0.98,0.85,0.92,1.18,1.66,1.18,1.23 215 | KANM800103,1.45,0.7,0.91,1.29,1.2,0.53,1.13,1.23,1.27,1.56,1.83,0.64,0.21,1.14,1.15,0.48,0.77,1.1,1.17,0.74 216 | KANM800104,0.75,1.46,0.31,0.46,1.37,0.83,0.83,1.87,0.66,1.56,0.86,0.33,0.52,0.75,0.79,0.82,1.36,2,0.79,1.08 217 | KARP850101,1.041,0.96,1.033,1.094,0.93,1.142,0.982,1.002,1.093,0.967,0.947,1.117,1.055,1.165,1.038,1.169,1.073,0.982,0.925,0.961 218 | KARP850102,0.946,0.878,1.089,1.036,0.912,1.042,0.952,0.892,1.082,0.961,0.862,1.006,1.085,1.025,1.028,1.048,1.051,0.927,0.917,0.93 219 | KARP850103,0.892,0.925,0.932,0.933,0.914,0.923,0.894,0.872,1.057,0.921,0.804,0.93,0.932,0.885,0.901,0.923,0.934,0.913,0.803,0.837 220 | KARS160101,-0.21,-6.04,1.36,2.3,-4.65,0,-1.23,-4.81,3.88,-4.68,-3.66,0.96,0.75,1.52,2.11,1.74,0.78,-3.5,-3.32,-1.01 221 | KARS160102,1,2,4,5,8,0,6,4,5,4,4,4,4,5,7,2,3,3,12,9 222 | KARS160103,2,4,8,10,14,0,14,8,10,8,8,8,8,10,12,4,6,6,24,18 223 | KARS160104,1,2,4,5,6,1,6,4,4,4,4,4,4,4,6,2,3,3,8,7 224 | KARS160105,1,2.33,5.17,6,7,0,6.71,3.25,7,5,5.4,5,4,5.86,8.12,1.67,3.25,3.25,11.1,8.88 225 | KARS160106,1,1,3,4,6,0,6,3,5,3,3,3,4,4,6,2,1,1,9,6 226 | KARS160107,1,3,6,8,11,0,9,6,9,6,7,6,4,8,12,3,4,4,14,13 227 | KARS160108,1,1.33,1.6,1.66,1.75,0,2,1.6,1.66,1.6,1.6,1.6,2,1.66,1.5,1.33,1.5,1.5,2.182,2 228 | KARS160109,2,6.243,11.539,11.53,14.851,0,12.876,10.851,10.363,11.029,9.49,11.539,12,12.207,12.499,5,9.928,9.928,13.511,12.868 229 | KARS160110,0,-2.243,-4.178,-3.425,-4.801,0,-3.721,-6.085,-3.151,-4.729,-2.812,-4.178,-4,-4.255,-4.307,1,-3.928,-3.928,-6.324,-4.793 230 | KARS160111,1,2,3,3.33,4.25,0,4.286,1.8,3,3.2,2.8,3.2,4,3.33,3.5,2,3,3,4,4.33 231 | KARS160112,2,2,0.528,-0.538,-1.672,0,-1.185,-1.517,-0.536,1.052,0.678,0.528,4,-1.043,-2.59,2,3,3,-2.576,-2.054 232 | KARS160113,6,6,12,12,18,1,15,12,12,12,18,12,12,12,19,6,6,6,24,18 233 | KARS160114,6,16.67,16.4,21,23.25,3.5,23.1,15.6,24.5,15.6,27.2,16.5,12,21.167,31.44,31.33,12.4,10.5,27.5,27.78 234 | KARS160115,6,12,12,14,18,1,18,12,18,12,18,14,12,15,20,8,8,6,18,20 235 | KARS160116,6,22,20,26,24,6,31,18,31,18,34,20,12,24,38,20,14,12,36,38 236 | KARS160117,12,28,34,40,48,7,47,30,37,30,40,33.007,24,39,45,22,27,24.007,68,56 237 | KARS160118,6,9.33,6.8,6.67,6,3.5,4.7,6,6.17,6,8,6.6,6,6.5,5,7.33,5.4,6,5.667,6.22 238 | KARS160119,12,28,28.634,28.731,26.993,7,24.243,24.841,22.739,25.021,31.344,27.708,24,27.831,23.343,20,23.819,24,29.778,28.252 239 | KARS160120,0,0,0,0,0,0,-1.734,-1.641,-0.179,0,0,0,0,0,0,0,-4.227,0,0.211,-0.96 240 | KARS160121,6,11.33,10.4,10.66,12,3.5,10.4,9.6,10.167,9.6,13.6,10,12,10.5,10.667,8.667,9,9,12.75,12.222 241 | KARS160122,0,6,2.969,1.822,2.026,0,1.605,3.373,1.372,3.113,2.656,3,12,1.849,4.2,6,6,6,2.044,1.599 242 | KHAG800101,49.1,0,0,0,54.7,64.6,75.7,18.9,0,15.6,6.8,-3.6,43.8,20,133,44.4,31,29.5,70.5,0 243 | KIDA850101,-0.27,-1.05,0.81,1.17,-1.43,-0.16,0.28,-0.77,1.7,-1.1,-0.73,0.81,-0.75,1.1,1.87,0.42,0.63,-0.4,-1.57,-0.56 244 | KIMC930101,-0.35,-0.47,-0.41,-0.41,-0.55,0,-0.46,-0.56,-0.41,-0.48,-0.46,-0.38,-0.23,-0.4,-0.44,-0.39,-0.48,-0.53,-0.48,-0.5 245 | KLEP840101,0,0,-1,-1,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0 246 | KOEP990101,-0.04,0.57,0.27,-0.33,-0.01,1.24,-0.11,-0.26,-0.18,-0.38,-0.09,0.25,0,-0.02,-0.3,0.15,0.39,-0.06,0.21,0.05 247 | KOEP990102,-0.12,-0.63,1.12,0.91,-0.67,0.76,1.34,-0.77,0.29,0.15,-0.71,1.05,0,1.67,0.34,1.45,-0.7,-0.7,-0.14,-0.49 248 | KRIW710101,4.6,-1,5.7,5.6,3.2,7.6,4.5,2.6,7.9,3.25,1.4,5.9,7,6.1,6.5,5.25,4.8,3.4,4,4.35 249 | KRIW790101,4.32,1.73,6.04,6.17,2.59,6.09,5.66,2.31,7.92,3.93,2.44,6.24,7.19,6.13,6.55,5.37,5.16,3.31,2.78,3.58 250 | KRIW790102,0.28,0.11,0.33,0.37,0.1,0.28,0.23,0.12,0.59,0.16,0.08,0.31,0.46,0.39,0.34,0.27,0.26,0.22,0.15,0.25 251 | KRIW790103,27.5,44.6,40,62,115.5,0,79,93.5,100,93.5,94.1,58.7,41.9,80.7,105,29.3,51.3,71.5,145.5,117.3 252 | KUHL950101,0.78,0.55,1.35,1.45,0.47,0.68,0.99,0.47,1.1,0.56,0.66,1.2,0.69,1.19,1.58,1,1.05,0.51,0.7,1 253 | KUMS000101,8.9,0.6,6.3,6.9,3.3,9.4,2.2,7,6.1,7.4,2.3,4.4,4.2,2.8,4.6,4,5.7,8.2,1.3,4.5 254 | KUMS000102,9.2,1,6,6,3.4,9.4,2.1,6,6.5,7.7,2.4,5.1,4.2,2.9,3.6,5.5,5.7,8.2,1.2,3.7 255 | KUMS000103,14.1,0.1,5.7,8.8,5,4.1,2,7.1,7.7,9.1,3.3,3.2,0.7,3.7,5.5,3.9,4.4,5.9,1.2,4.5 256 | KUMS000104,13.4,0.8,4.6,7.8,4.5,4.6,3.3,6.5,7.5,10.6,3,3.7,1.3,4.8,3.9,3.8,4.6,7.1,1,3.3 257 | KYTJ820101,1.8,2.5,-3.5,-3.5,2.8,-0.4,-3.2,4.5,-3.9,3.8,1.9,-3.5,-1.6,-3.5,-4.5,-0.8,-0.7,4.2,-0.9,-1.3 258 | LAWE840101,-0.48,-0.32,-0.75,-0.71,1.03,0,-0.51,0.81,-0.09,1.02,0.81,-0.87,2.03,-0.32,-0.06,0.05,-0.35,0.56,0.66,1.24 259 | LEVM760101,-0.5,-1,2.5,2.5,-2.5,0,-0.5,-1.8,3,-1.8,-1.3,0.2,-1.4,0.2,3,0.3,-0.4,-1.5,-3.4,-2.3 260 | LEVM760102,0.77,1.38,1.99,2.63,2.97,0,2.76,1.83,2.94,2.08,2.34,1.98,1.42,2.58,3.72,1.28,1.43,1.49,3.58,3.36 261 | LEVM760103,121.9,113.7,121.2,118.2,118.2,0,118.2,118.9,122,118.1,113.1,117.5,81.9,118,121.4,117.9,117.1,121.7,118.4,110 262 | LEVM760104,243.2,209.4,215,213.6,203.7,300,219.9,217.9,210.9,205.6,204,207.1,237.4,205.4,206.6,232,226.7,220.3,203.7,195.6 263 | LEVM760105,0.77,1.22,1.43,1.77,1.9,0.58,1.78,1.56,2.08,1.54,1.8,1.45,1.25,1.75,2.38,1.08,1.24,1.29,2.21,2.13 264 | LEVM760106,5.2,6.1,5,6,7.1,4.2,6,7,6,7,6.8,5,6.2,6,6,4.9,5,6.4,7.6,7.1 265 | LEVM760107,0.025,0.1,0.1,0.1,0.39,0.025,0.1,0.19,0.2,0.19,0.19,0.1,0.17,0.1,0.2,0.025,0.1,0.15,0.56,0.39 266 | LEVM780101,1.29,1.11,1.04,1.44,1.07,0.56,1.22,0.97,1.23,1.3,1.47,0.9,0.52,1.27,0.96,0.82,0.82,0.91,0.99,0.72 267 | LEVM780102,0.9,0.74,0.72,0.75,1.32,0.92,1.08,1.45,0.77,1.02,0.97,0.76,0.64,0.8,0.99,0.95,1.21,1.49,1.14,1.25 268 | LEVM780103,0.77,0.81,1.41,0.99,0.59,1.64,0.68,0.51,0.96,0.58,0.41,1.28,1.91,0.98,0.88,1.32,1.04,0.47,0.76,1.05 269 | LEVM780104,1.32,0.92,1.03,1.44,1.02,0.61,1.31,0.93,1.25,1.31,1.39,0.95,0.58,1.1,0.98,0.76,0.79,0.93,0.97,0.73 270 | LEVM780105,0.86,1.04,0.69,0.66,1.21,0.89,0.85,1.47,0.77,1.04,0.93,0.73,0.68,1,0.97,1.02,1.27,1.43,1.26,1.31 271 | LEVM780106,0.79,0.79,1.47,1.02,0.77,1.67,0.81,0.5,0.99,0.57,0.51,1.25,1.78,0.92,0.9,1.3,0.97,0.46,0.79,0.93 272 | LEWP710101,0.22,0.2,0.73,0.08,0.08,0.58,0.14,0.22,0.27,0.19,0.38,0.42,0.46,0.26,0.28,0.55,0.49,0.08,0.43,0.46 273 | LIFS790101,0.92,1.16,0.48,0.61,1.25,0.61,0.93,1.81,0.7,1.3,1.19,0.6,0.4,0.95,0.93,0.82,1.12,1.81,1.54,1.53 274 | LIFS790102,1,0.91,0.5,0.59,1.3,0.79,0.38,2.6,0.59,1.42,1.49,0.54,0.35,0.28,0.68,0.7,0.59,2.63,0.89,1.08 275 | LIFS790103,0.9,1.24,0.47,0.62,1.23,0.56,1.12,1.54,0.74,1.26,1.09,0.62,0.42,1.18,1.02,0.87,1.3,1.53,1.75,1.68 276 | MANP780101,12.97,14.63,10.85,11.89,14,12.43,12.16,15.67,11.36,14.9,14.39,11.42,11.37,11.76,11.72,11.23,11.69,15.71,13.93,13.42 277 | MAXF760101,1.43,0.94,0.92,1.67,1.19,0.46,0.98,1.04,1.27,1.36,1.53,0.64,0.49,1.22,1.18,0.7,0.78,0.98,1.01,0.69 278 | MAXF760102,0.86,1.17,0.72,0.62,1.16,0.97,1.06,1.24,0.79,0.98,1.08,0.74,1.22,0.89,0.94,1.04,1.18,1.33,1.07,1.25 279 | MAXF760103,0.64,0.32,1.92,1.01,0.86,0.63,2.05,0.92,0.89,0.37,1.07,3.14,0.5,0.8,0.62,1.01,0.92,0.87,1,1.31 280 | MAXF760104,0.17,0.95,1.08,0.28,0.28,5.02,0.57,0.26,1.17,0.21,0,2.62,0.12,0.91,0.76,0.57,0.23,0.24,0,0.97 281 | MAXF760105,1.13,0.38,1.18,1.02,0.45,3.84,0.3,0.4,1.13,0.65,0,1.11,0,0.41,0.48,0.81,0.71,0.48,0.93,0.38 282 | MAXF760106,1,1.09,1.39,1.04,0.65,0.46,0.71,0.68,1.05,1.01,0.36,0.87,1.95,1.13,1.18,1.56,1.23,0.58,1.1,0.87 283 | MCMT640101,4.34,35.77,12,17.26,29.4,0,21.81,19.06,21.29,18.78,21.64,13.28,10.93,17.56,26.66,6.35,11.01,13.92,42.53,31.53 284 | MEEJ800101,0.5,-6.8,-8.2,-16.9,13.2,0,-3.5,13.9,0.1,8.8,4.8,0.8,6.1,-4.8,0.8,1.2,2.7,2.7,14.9,6.1 285 | MEEJ800102,-0.1,-2.2,-2.8,-7.5,13.9,-0.5,0.8,11.8,-3.2,10,7.1,-1.6,8,-2.5,-4.5,-3.7,1.5,3.3,18.1,8.2 286 | MEEJ810101,1.1,7.1,-1.6,0.7,13.4,-0.2,-0.7,8.5,-1.9,11,5.4,-4.2,4.4,-2.9,-0.4,-3.2,-1.7,5.9,17.1,7.4 287 | MEEJ810102,1,4.6,-0.5,1.1,12.6,0.2,-2.2,7,-3,9.6,4,-3,3.1,-2,-2,-2.9,-0.6,4.6,15.1,6.7 288 | MEIH800101,0.93,0.88,1.01,1.02,0.78,1.01,0.89,0.79,1.05,0.85,0.84,0.98,1,1.02,0.98,1.02,0.99,0.81,0.83,0.93 289 | MEIH800102,0.94,0.84,1.08,1.12,0.73,1.01,0.92,0.76,1.23,0.82,0.83,1.04,1.04,1.11,1.09,1.04,1.02,0.81,0.87,1.03 290 | MEIH800103,87,104,71,72,108,90,90,105,65,104,100,70,78,66,81,83,83,94,94,83 291 | MITS020101,0,0,0,1.27,0,0,1.45,0,3.67,0,0,0,0,1.25,2.45,0,0,0,6.93,5.06 292 | MIYS850101,2.36,3.36,1.67,1.74,4.37,2.06,2.41,4.17,1.23,3.93,4.22,1.7,1.89,1.75,1.92,1.81,2.04,3.49,3.82,2.91 293 | MIYS990101,-0.02,-0.96,0.72,0.74,-2.22,0.38,0,-1.89,1.01,-2.29,-1.36,0.63,0.47,0.56,0.44,0.55,0.25,-1.34,-1.28,-0.88 294 | MIYS990102,0,-0.16,0.12,0.12,-0.36,0.06,0,-0.31,0.17,-0.37,-0.22,0.1,0.08,0.09,0.07,0.09,0.04,-0.22,-0.21,-0.14 295 | MIYS990103,-0.03,-0.36,0.17,0.23,-0.34,0.09,-0.04,-0.33,0.32,-0.38,-0.3,0.13,0.2,0.13,0.09,0.1,0.01,-0.29,-0.24,-0.23 296 | MIYS990104,-0.04,-0.38,0.19,0.23,-0.38,0.09,-0.04,-0.34,0.33,-0.37,-0.3,0.13,0.19,0.14,0.07,0.12,0.03,-0.29,-0.33,-0.29 297 | MIYS990105,-0.02,-0.32,0.19,0.21,-0.33,-0.02,-0.02,-0.28,0.3,-0.32,-0.25,0.1,0.11,0.15,0.08,0.11,0.05,-0.23,-0.27,-0.23 298 | MONM990101,0.5,0.6,1.6,1.6,0.4,1.3,1.6,0.6,1.6,0.4,0.5,1.7,1.7,1.6,1.7,0.7,0.4,0.5,0.7,0.6 299 | MONM990201,0.4,0.7,1.5,1.3,0.3,1.1,1.4,0.5,1.4,0.3,0.5,1.6,1.6,1.4,1.5,0.9,0.7,0.4,0.9,0.9 300 | MUNV940101,0.423,0.877,0.87,0.167,0.706,1.162,0.802,0.566,0.615,0.494,0.444,0.906,1.945,0.594,0.503,0.928,0.884,0.706,0.69,0.778 301 | MUNV940102,0.619,1.107,0.932,0.675,0.968,1.361,1.034,0.876,0.784,0.74,0.736,1.089,1.78,0.77,0.753,0.969,1.053,0.939,0.91,1.009 302 | MUNV940103,1.08,0.733,1.266,1.085,0.685,1.104,0.906,0.583,1.026,0.789,0.812,1.197,1.412,1.05,0.976,0.987,0.784,0.546,0.755,0.665 303 | MUNV940104,0.978,0.573,1.038,0.962,0.585,1.405,0.724,0.502,0.841,0.766,0.729,0.915,2.613,0.863,0.784,0.784,0.569,0.444,0.671,0.56 304 | MUNV940105,1.4,1.14,1.89,1.42,1.07,2.06,1.25,1.02,1.34,1.33,1.12,1.61,3.9,1.33,1.23,1.2,0.99,0.87,1.1,0.98 305 | NADH010101,58,116,-97,-131,92,-11,-73,107,-24,95,78,-93,-79,-139,-184,-34,-7,100,59,-11 306 | NADH010102,51,137,-78,-115,108,-13,-55,106,-205,103,73,-84,-79,-128,-144,-26,-3,108,69,11 307 | NADH010103,41,169,-47,-90,128,-18,-35,104,-148,103,77,-74,-81,-104,-109,-31,10,116,102,36 308 | NADH010104,32,182,-29,-74,132,-22,-25,106,-124,104,82,-73,-82,-95,-95,-34,20,113,118,44 309 | NADH010105,24,194,0,-57,131,-28,-31,102,-9,103,90,-76,-85,-87,-79,-36,34,111,116,43 310 | NADH010106,5,224,45,-8,117,-47,-50,83,-38,82,83,-77,-103,-67,-57,-41,79,117,130,27 311 | NADH010107,-2,329,248,117,120,-66,-70,28,115,36,62,-97,-132,-37,-41,-52,174,114,179,-7 312 | NAGK730101,1.29,0.94,1,1.54,1.23,0.72,1.29,0.94,1.23,1.23,1.23,0.77,0.7,1.1,0.83,0.78,0.87,0.97,1.06,0.63 313 | NAGK730102,0.96,1.13,0.9,0.33,1.37,0.9,0.87,1.54,0.81,1.26,1.29,0.72,0.75,1.18,0.67,0.77,1.23,1.41,1.13,1.07 314 | NAGK730103,0.72,1.01,1.04,0.75,0.58,1.35,0.76,0.8,0.84,0.63,0.62,1.38,1.43,0.81,1.33,1.34,1.03,0.83,0.87,1.35 315 | NAKH900101,7.99,1.81,5.14,6.1,3.83,6.91,2.17,5.48,6.01,9.16,2.5,4.33,4.95,3.98,5.86,6.84,5.77,6.65,1.34,3.15 316 | NAKH900102,3.73,2.3,2.23,3,1.94,3.36,1.55,2.52,3.36,3.4,1.37,2.33,3.18,2.36,3.34,2.83,2.63,2.53,1.15,1.76 317 | NAKH900103,5.74,1.03,2.11,2.63,6.51,5.66,2.3,9.12,3.2,15.36,5.3,5.25,4.79,2.3,1.92,7.55,7.51,5.12,2.51,4.08 318 | NAKH900104,-0.6,-0.34,-1.36,-1.16,1.38,-0.37,0.08,1.44,-0.84,1.82,2.04,0.39,-0.05,-0.71,-1.18,0.25,0.66,-0.6,1.02,0.53 319 | NAKH900105,5.88,1.11,1.7,2.6,6.58,5.29,2.33,8.78,2.58,16.52,6,4.38,5.29,2.3,1.54,7.68,8.38,4.66,2.89,3.51 320 | NAKH900106,-0.57,-0.3,-1.54,-1.17,1.42,-0.48,0.1,1.31,-1.02,2.16,2.55,0.02,0.11,-0.71,-1.29,0.3,0.99,-0.79,1.35,0.2 321 | NAKH900107,5.39,0.86,3.07,2.7,6.34,6.52,2.23,9.94,4.67,12.64,3.68,7.31,3.62,2.31,2.81,7.24,5.44,6.18,1.64,5.42 322 | NAKH900108,-0.7,-0.41,-0.93,-1.13,1.29,-0.12,0.04,1.77,-0.4,1.02,0.86,1.28,-0.42,-0.71,-0.91,0.14,-0.13,-0.19,0.26,1.29 323 | NAKH900109,9.25,1.07,3.89,4.8,6.36,8.51,1.88,6.47,3.5,10.94,3.14,3.71,4.36,3.17,3.96,6.26,5.66,7.55,2.22,3.28 324 | 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NAKH920105,9.9,2.55,0.35,0.08,6.47,8.14,0.2,15.25,0.16,22.28,1.85,0.94,2.38,0.87,0.09,4.17,4.33,14.34,2.21,3.42 333 | NAKH920106,6.69,1.7,4.97,7.76,3.59,6.32,2.11,4.51,8.36,8.23,2.46,4.49,5.2,5.39,6.65,7.4,5.18,5.27,1.06,2.75 334 | NAKH920107,5.08,2.95,5.96,6.04,4.36,8.2,2.1,4.95,4.93,8.03,2.61,5.75,4.84,4.24,4.75,6.41,5.87,6.07,2.31,4.55 335 | NAKH920108,9.36,2.56,0.94,0.94,10.99,6.17,0.47,13.73,0.58,16.64,3.93,2.31,1.96,1.14,0.27,5.58,4.68,12.43,2.2,3.13 336 | NISK800101,0.23,1.78,-1.13,-0.75,0.48,-0.07,0.11,1.19,-1.05,1.03,0.66,-0.94,-0.76,-0.57,-0.26,-0.67,-0.36,1.24,0.9,0.59 337 | NISK860101,-0.22,4.66,-4.12,-3.64,5.27,-1.62,1.28,5.58,-4.18,5.01,3.51,-2.65,-3.03,-2.76,-0.93,-2.84,-1.2,4.45,5.2,2.15 338 | NOZY710101,0.5,0,0,0,2.5,0,0.5,1.8,0,1.8,1.3,0,0,0,0,0,0.4,1.5,3.4,2.3 339 | OLSK800101,1.38,1.43,0.52,0.71,1.72,1.34,0.66,2.32,0.15,1.47,1.78,0.37,0.85,0.22,0,0.86,0.89,1.99,0.82,0.47 340 | ONEK900101,13.4,11.6,11.7,12.2,12.1,11.3,11.6,12,13,13,12.8,12,6.5,12.8,13.3,12.2,11.7,11.9,12.4,12.1 341 | ONEK900102,-0.77,-0.23,-0.15,-0.27,-0.41,0,-0.06,-0.23,-0.65,-0.62,-0.5,-0.07,3,-0.33,-0.68,-0.35,-0.11,-0.14,-0.45,-0.17 342 | OOBM770101,-1.895,-2.035,-1.518,-1.535,-1.864,-1.898,-1.755,-1.951,-1.374,-1.966,-1.963,-1.56,-1.699,-1.521,-1.475,-1.753,-1.767,-1.981,-1.869,-1.686 343 | OOBM770102,-1.404,-1.365,-1.162,-1.163,-1.135,-1.364,-1.215,-1.189,-1.074,-1.315,-1.303,-1.178,-1.236,-1.116,-0.921,-1.297,-1.252,-1.254,-1.03,-1.03 344 | OOBM770103,-0.491,-0.67,-0.356,-0.371,-0.729,-0.534,-0.54,-0.762,-0.3,-0.65,-0.659,-0.382,-0.463,-0.405,-0.554,-0.455,-0.515,-0.728,-0.839,-0.656 345 | OOBM770104,-9.475,-12.21,-12.144,-13.815,-20.504,-7.592,-17.55,-15.608,-12.366,-15.728,-15.704,-12.48,-11.893,-13.689,-16.225,-10.518,-12.369,-13.867,-26.166,-20.232 346 | 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PALJ810103,0.81,1.12,0.71,0.59,1.13,0.94,0.85,1.47,0.77,1.03,0.96,0.81,0.75,1.03,1.03,1.02,1.19,1.44,1.24,1.35 355 | PALJ810104,0.9,1.12,0.75,0.44,1.41,0.83,0.86,1.59,0.75,1.24,0.94,0.82,0.46,0.95,0.75,0.7,1.2,1.73,1.28,1.45 356 | PALJ810105,0.84,0.69,1.28,0.78,0.88,1.76,0.53,0.55,0.95,0.49,0.52,1.48,1.47,1,0.91,1.29,1.05,0.51,0.88,1.28 357 | PALJ810106,0.65,1.43,1.47,0.75,0.72,1.53,0.96,0.57,0.95,0.56,0.71,1.45,1.51,0.94,0.93,1.46,0.96,0.55,0.9,1.12 358 | PALJ810107,1.08,1.22,0.86,1.09,0.96,0.85,1.02,0.98,1.01,1.04,1.11,1.05,0.91,0.95,0.93,0.95,1.15,1.03,1.17,0.8 359 | PALJ810108,1.34,1.27,1.06,1.69,1.02,0.47,1.11,0.84,1.08,1.39,0.9,0.83,0.48,1.13,0.91,1.05,0.74,1.18,0.64,0.73 360 | PALJ810109,1.15,1.03,1,1.37,0.92,0.64,0.95,0.99,1.2,1.22,1.45,0.87,0.72,1.43,1.06,0.84,0.97,0.82,1.11,0.72 361 | PALJ810110,0.89,1.04,0.71,0.72,1.32,0.87,1.04,1.14,1,1.02,1.41,0.67,0.69,1.06,1.06,0.86,1.15,1.66,1.06,1.35 362 | 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PARS000102,0.32,0.198,0.424,0.514,0.314,0.374,0.299,0.306,0.446,0.34,0.313,0.384,0.354,0.436,0.327,0.376,0.339,0.294,0.291,0.287 371 | PLIV810101,-2.89,-2.49,-3.38,-2.94,-1.63,-3.25,-2.84,-1.72,-3.31,-1.61,-1.84,-3.41,-2.5,-3.15,-3.3,-3.3,-2.91,-2.08,-1.75,-2.42 372 | PONJ960101,91.5,114.4,135.2,154.6,198.8,67.5,163.2,162.6,162.5,163.4,165.9,138.3,123.4,156.4,196.1,102,126,138.4,209.8,237.2 373 | PONP800101,12.28,14.93,10.97,11.19,13.43,12.01,12.84,14.77,10.8,14.1,14.33,11,11.19,11.28,11.49,11.26,11.65,15.07,12.95,13.29 374 | PONP800102,7.62,10.93,6.18,6.38,8.99,7.31,7.85,9.99,5.72,9.37,9.83,6.17,6.64,6.67,6.81,6.93,7.08,10.38,8.41,8.53 375 | PONP800103,2.63,3.36,2.29,2.31,3.02,2.55,2.57,3.08,2.12,2.98,3.18,2.27,2.46,2.45,2.45,2.6,2.55,3.21,2.85,2.79 376 | PONP800104,13.65,14.49,10.98,12.55,14.08,15.36,11.59,14.63,11.96,14.01,13.4,12.24,11.51,11.3,11.28,11.26,13,12.88,12.06,12.64 377 | 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WOEC730101,7,5.5,13,12.5,5,7.9,8.4,4.9,10.1,4.9,5.3,10,6.6,8.6,9.1,7.5,6.6,5.6,5.3,5.7 537 | WOLR790101,1.12,0.59,-0.83,-0.92,0.67,1.2,-0.93,1.16,-0.8,1.18,0.55,-0.83,0.54,-0.78,-2.55,-0.05,-0.02,1.13,-0.19,-0.23 538 | WOLR810101,1.94,-1.24,-10.95,-10.2,-0.76,2.39,-10.27,2.15,-9.52,2.28,-1.48,-9.68,-3.68,-9.38,-19.92,-5.06,-4.88,1.99,-5.88,-6.11 539 | WOLS870101,0.07,0.71,3.64,3.08,-4.92,2.23,2.41,-4.44,2.84,-4.19,-2.49,3.22,-1.22,2.18,2.88,1.96,0.92,-2.69,-4.75,-1.39 540 | WOLS870102,-1.73,-0.97,1.13,0.39,1.3,-5.36,1.74,-1.68,1.41,-1.03,-0.27,1.45,0.88,0.53,2.52,-1.63,-2.09,-2.53,3.65,2.32 541 | WOLS870103,0.09,4.13,2.36,-0.07,0.45,0.3,1.11,-1.03,-3.14,-0.98,-0.41,0.84,2.23,-1.14,-3.44,0.57,-1.4,-1.29,0.85,0.01 542 | YUTK870101,8.5,11,8.5,8.8,11.2,7.1,10.1,16.8,7.9,15,13.3,8.2,8.2,6.3,0,7.4,8.8,12,9.9,8.8 543 | YUTK870102,6.8,8.3,7,4.9,8.3,6.4,9.2,10,7.5,12.2,8.4,6.2,6.9,8.5,0,8,7,9.4,5.7,6.8 544 | YUTK870103,18.08,18.17,17.36,18.16,17.3,18.24,18.49,18.62,17.96,18.6,18.11,17.47,18.16,17.93,0,17.57,17.54,18.3,17.19,17.99 545 | YUTK870104,18.56,17.84,17.94,17.97,17.95,18.57,18.64,19.21,18.36,19.01,18.49,18.24,18.77,18.51,0,18.06,17.71,18.98,16.87,18.23 546 | ZASB820101,-0.152,0,-0.355,-0.411,0.001,-0.19,0,-0.086,-0.062,-0.102,-0.107,-0.203,-0.181,-0.181,-0.089,-0.203,-0.17,-0.125,0.275,0 547 | ZHOH040101,2.18,3.89,1.75,1.89,5.88,1.17,2.51,4.5,2.12,4.71,3.63,1.85,2.09,2.16,2.71,1.66,2.18,3.77,6.46,5.01 548 | ZHOH040102,1.79,2.22,2.33,2.52,4.84,0.7,3.06,4.59,2.5,4.72,3.91,2.83,2.45,2.37,3.2,1.82,2.45,3.67,5.64,4.46 549 | ZHOH040103,13.4,22.6,8.2,7.3,23.9,7,11.3,20.3,6.1,20.8,15.7,7.6,9.9,8.5,8.5,8.2,10.3,19.5,24.5,19.5 550 | ZIMJ680101,0.83,1.48,0.64,0.65,2.75,0.1,1.1,3.07,1.6,2.52,1.4,0.09,2.7,0,0.83,0.14,0.54,1.79,0.31,2.97 551 | ZIMJ680102,11.5,13.46,11.68,13.57,19.8,3.4,13.69,21.4,15.71,21.4,16.25,12.82,17.43,14.45,14.28,9.47,15.77,21.57,21.67,18.03 552 | ZIMJ680103,0,1.48,49.7,49.9,0.35,0,51.6,0.13,49.5,0.13,1.43,3.38,1.58,3.53,52,1.67,1.66,0.13,2.1,1.61 553 | ZIMJ680104,6,5.05,2.77,3.22,5.48,5.97,7.59,6.02,9.74,5.98,5.74,5.41,6.3,5.65,10.76,5.68,5.66,5.96,5.89,5.66 554 | ZIMJ680105,9.9,2.8,2.8,3.2,18.8,5.6,8.2,17.1,3.5,17.6,14.9,5.4,14.8,9,4.6,6.9,9.5,14.3,17.1,15 555 | -------------------------------------------------------------------------------- /Standalone/Data/aaindices.csv: -------------------------------------------------------------------------------- 1 | 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-------------------------------------------------------------------------------- /Standalone/Data/atom.csv: -------------------------------------------------------------------------------- 1 | A,CHHHCHNHHCOOH 2 | R,HNCNHHNHCHHCHHCHHCHNHHCOOH 3 | N,HHNCOCHHCHNHHCOOH 4 | D,HOOCCHHCHNHHCOOH 5 | C,HSCHHCHNHHCOOH 6 | Q,HHNCOCHHCHHCHNHHCOOH 7 | E,HOOCCHHCHHCHNHHCOOH 8 | G,NHHCHHCOOH 9 | H,NHCHNCHCCHHCHNHHCOOH 10 | I,CHHHCHHCHCHHHCHNHHCOOH 11 | L,CHHHCHHHCHCHHCHNHHCOOH 12 | K,HHNCHHCHHCHHCHHCHNHHCOOH 13 | M,CHHHSCHHCHHCHNHHCOOH 14 | F,CCCCCCHHHHHCHHCHNHHCOOH 15 | P,NHCHHCHHCHHCHCOOH 16 | S,HOCHHCHNHHCOOH 17 | T,CHHHCHOHCHNHHCOOH 18 | W,CCCCCCHHHHHNHCHCCHHCHNHHCOOH 19 | Y,HOCCCCCCHHHHHCHHCHNHHCOOH 20 | V,CHHHCHHHCHCHNHHCOOH 21 | -------------------------------------------------------------------------------- /Standalone/Data/bonds.csv: -------------------------------------------------------------------------------- 1 | Name,nBonds_tot,Hydrogen_bonds,nBondsS,nBondsD 2 | G,9,5,8,1 3 | S,13,7,12,1 4 | A,12,7,11,1 5 | D,15,7,13,2 6 | N,16,8,14,2 7 | T,16,9,15,1 8 | P,17,9,16,1 9 | E,18,9,16,2 10 | V,18,11,17,1 11 | Q,19,10,17,2 12 | M,19,11,18,1 13 | H,20,9,17,3 14 | I,21,13,20,1 15 | Y,24,11,20,4 16 | L,21,13,20,1 17 | K,23,14,22,1 18 | W,28,12,23,5 19 | F,23,11,19,4 20 | C,25,12,23,2 21 | R,25,14,23,2 22 | -------------------------------------------------------------------------------- /Standalone/Data/can_pat.csv: -------------------------------------------------------------------------------- 1 | Name,canonical_pattern 2 | G,--=-- 3 | S,---=--- 4 | A,---=-- 5 | D,---=----=- 6 | N,---=----=- 7 | T,----=--- 8 | P,c--=- 9 | E,---=----=-- 10 | V,-----=-- 11 | Q,---=----=-- 12 | M,------=-- 13 | H,c----=-- 14 | I,------=-- 15 | Y,b----=--- 16 | L,------=-- 17 | K,------=-- 18 | W,c----=-- 19 | F,b----=-- 20 | C,---=--------=-- 21 | R,---=---=-- 22 | -------------------------------------------------------------------------------- /Standalone/Data/data: -------------------------------------------------------------------------------- 1 | # A C D E F G H I K L M N P Q R S T V W Y 2 | Hydrophobicity 0.62 0.29 -0.9 -0.74 1.19 0.48 -0.4 1.38 -1.5 1.06 0.64 -0.78 0.12 -0.85 -2.53 -0.18 -0.05 1.08 0.81 0.26 3 | Hydrophilicity -0.5 -1 3 3 -2.5 0 -0.5 -1.8 3 -1.8 -1.3 0.2 0 0.2 3 0.3 -0.4 -1.5 -3.4 -2.3 4 | SideChainMass 15 47 59 73 91 1 82 57 73 57 75 58 42 72 101 31 45 43 130 107 5 | -------------------------------------------------------------------------------- /Standalone/LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | 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But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /Standalone/Pfeature_Descriptors.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raghavagps/Pfeature/1117d4c9712a7d230ed0e0026be8d9a2d859e978/Standalone/Pfeature_Descriptors.pdf -------------------------------------------------------------------------------- /Standalone/README.md: -------------------------------------------------------------------------------- 1 | # Standalone Package of Pfeature 2 | ## Introduction 3 | Pfeature is developed for computing wide range of protein and peptides features from their amino acid sequences, and structures. More information on Pfeature is available from its web server https://webs.iiitd.edu.in/raghava/pfeature. The standalone package of Pfeature allow users to computes individual as well as, all possible descriptors for a protein/peptide sequence. This page provide information about standalone version of Pfeature. This standalone contains three scripts, their description is as follows: 4 | - `pfeature_comp.py` : To calculated composition based features 5 | - `pfeature_bin.py` : To calculated binary profile based features 6 | - `pfeature_pssm.py` : To calculated binary profile based features 7 | 8 | ## Help Usage 9 | To learn about the full usage, run the following command: 10 | ```sh 11 | python pfeature_comp.py -h 12 | OR 13 | python pfeature_bin.py -h 14 | OR 15 | python pfeature_pssm.py -h 16 | ``` 17 | Following output will be generated on running python "pfeature_bin.py -h" command:
18 | ![Screenshot](Screenshot.png) 19 | 20 | ### Parameters Description 21 | ``` 22 | Input File: It allow users to provide input in two format: 23 | i. FASTA format (standard) (e.g. protein.fa) 24 | ii. Simple Format, file should have sequences in a single line in single letter code (eg. protein.seq) 25 | 26 | Output File: Program will save result in CSV format, in the provided filename. 27 | If user do not provide output file name, it will be stored in pfeature_results.csv. 28 | In case user want to calculate all the features except ATB and BTB, the job name will be 'ALLBIN'. Reason to leave ATB and BTB is, the number of atoms and bonds are not equal in all amino acid residues. 29 | 30 | Job name: It allows users to choose the type of composition, the user want to calculate, such as AAB which stands for Amino Acid based binary profile. 31 | In case user do not provide any job name, it will choose AAB by default. 32 | 33 | N-terminal: It allows user to cut the specific number of residues from the N-terminal of the sequences. 34 | 35 | C-terminal: It allows user to cut the specific number of residues from the C-terminal of the sequences. 36 | 37 | NCT-terminal: It allows user to cut the specific number of residues from the N- and C-terminal of the sequences, and join them. 38 | 39 | Rest_N : It allow users to drop the specific number of residues from N-terminal, and perform operations on the rest. 40 | 41 | Rest_C : It allow users to drop the specific number of residues from C-terminal, and perform operations on the rest. 42 | 43 | Split: It allow users to divided the sequence into number of sequences. 44 | 45 | Lag : It defines the value for order of dipeptide, to calculate the dipeptide based binary profiles. 46 | ``` 47 | ## Minimum Usage Usage 48 | To learn about the full usage, run the following command: 49 | ```sh 50 | python pfeature_comp.py -i protein.fa 51 | OR 52 | python pfeature_bin.py -i protein.fa 53 | OR 54 | python pfeature_pssm.py -i protein.fa 55 | ``` 56 | 57 | ## Pfeature Package Files 58 | It contantain following files, brief description of these files are given below: 59 | 60 | * `LICENSE` : License information 61 | 62 | * `README.txt` : This file provide information about this package 63 | 64 | * `pfeature_comp.py` : Python program to calculate composition based features 65 | 66 | * `pfeature_bin.py` : Python program to calculate binary profile based features 67 | 68 | * `pfeature_pssm.py` : Python program to calculate pssm profile based features 69 | 70 | * `protein.seq` : Example file contain protein sequences in simple format 71 | 72 | * `protein.fa` : Example file contain protein sequences in FASTA format 73 | 74 | * `Data ` : This folder contains the files required to calcuate the composition and binary profile based features. 75 | 76 | * `envfile` : This file contains the path information required to run the pfeature_pssm.py script. 77 | 78 | * `Pfeature_Descriptors.pdf` : This file comprises of description of the header of output files, which is generated using the aforementioned scripts. 79 | 80 | * `Requirement.txt` : This file consists of commands and pre-requisite to run the aforementioned scripts. 81 | -------------------------------------------------------------------------------- /Standalone/README.txt: -------------------------------------------------------------------------------- 1 | # Pfeature 2 | # Introduction 3 | Pfeature is developed for computing wide range of protein and peptides features from their amino acid sequences. More information on Pfeature is abvailble from its web server https://webs.iiitd.edu.in/raghava/pfeature. This page provide information about standalone version of Pfeature. This standalone contains three scripts, their description is as follows: 4 | 5 | ############################################################################################################################################################################################################################# 6 | 7 | 1: Standalone for calculating composition based features: 8 | 9 | **Important: To run this script 'Data' folder should be in the same directory.** 10 | 11 | Minimum USAGE: Minimum ussage is "pfeature_comp.py -i protein.fa" where protein.fa is a input fasta file. This will calculate the amino acid composition of the seqeunces provided in the fasta file. It will use other parameters by default. It will save output in "pfeature_result.csv" in CSV (comma seperated variables). 12 | 13 | #Full Usage: Following is complete list of all options, you may get these options by "pfeature_comp.py -h" 14 | usage: pfeature_comp.py [-h] -i INPUT [-o OUTPUT] 15 | [-j {AAC,DPC,TPC,ATC,BTC,PCP,AAI,RRI,PRI,DDR,SEP,SER,SPC,ACR,CTC,CeTD,PAAC,APAAC,QSO,SOC,ALLCOMP}] 16 | [-n N_TERMINAL] [-c C_TERMINAL] [-nct NC_TERMINAL] 17 | [-rn REST_N] [-rc REST_C] [-s SPLIT] [-d LAG] 18 | [-w WEIGHT] [-t PWEIGHT] 19 | 20 | optional arguments: 21 | -h, --help show this help message and exit 22 | -i INPUT, --input INPUT 23 | Input: protein or protein.sequence in FASTA format or single sequence per line in single letter code 24 | -o OUTPUT, --output OUTPUT 25 | Output: File for saving results by default pfeature_result.csv 26 | -j {AAC,DPC,TPC,ATC,BTC,PCP,AAI,RRI,PRI,DDR,SEP,SER,SPC,ACR,CTC,CeTD,PAAC,APAAC,QSO,SOC,ALLCOMP}, --job {AAC,DPC,TPC,ATC,BTC,PCP,AAI,RRI,PRI,DDR,SEP,SER,SPC,ACR,CTC,CeTD,PAAC,APAAC,QSO,SOC,ALLCOMP} 27 | Job Type: 28 | AAC: Amino acid composition 29 | DPC: Dipeptide composition 30 | TPC: Tripeptide composition 31 | ATC: Atomic composition 32 | BTC: Bond composition 33 | PCP: Physico-chemical properties composition 34 | AAI: Amino-acid indices composition 35 | RRI: Residue repeat information 36 | PRI: Physico-chemical properties repeat information 37 | DDR: Distance distribution of residues 38 | SEP: Shannon entropy of protein 39 | SER: Shannon entropy of residues 40 | SPC: Shannon entropy of physico-chemical properties 41 | ACR: Autocorrelation descriptors 42 | CTC: Conjoint triad descriptors 43 | CeTD: Composition enhanced transition distribution 44 | PAAC: Pseudo amino acid composition 45 | APAAC: Amphiphilic pseudo amino acid composition 46 | QSO: Quasi sequence order 47 | SOC: Sequence order coupling number 48 | ALLCOMP:All composition features together except ACR and AAI 49 | by default AAC 50 | -n N_TERMINAL, --n_terminal N_TERMINAL 51 | Window Length from N-terminal: by default 0 52 | -c C_TERMINAL, --c_terminal C_TERMINAL 53 | Window Length from C-terminal: by default 0 54 | -nct NC_TERMINAL, --nc_terminal NC_TERMINAL 55 | Residues from N- and C-terminal: by default 0 56 | -rn REST_N, --rest_n REST_N 57 | Number of residues removed from N-terminal, by default 0 58 | -rc REST_C, --rest_c REST_C 59 | Number of residues removed from C-terminal, by default 0 60 | -s SPLIT, --split SPLIT 61 | Number of splits a sequence divided into, by default 0 62 | -d LAG, --lag LAG This represents the order of gap, lag or dipeptide, by default 1 63 | -w WEIGHT, --weight WEIGHT 64 | Weighting Factor for QSO: Value between 0 to 1, by default 0.1 65 | -t PWEIGHT, --pweight PWEIGHT 66 | Weighting factor for pseudo and amphiphlic pseudo amino acid composition: Value between 0 to 1, by default 0.05 67 | 68 | #Parameters Description: 69 | 70 | Input File: It allow users to provide input in two format; 71 | i) FASTA format (standard) (e.g. protein.fa) 72 | ii) Simple Format, in this case, file should have sequences in a single line in single letter code (eg. protein.seq). 73 | 74 | Output File: Program will save result in CSV format, in the provided filename. 75 | In case user do not provide output file name, it will be stored in pfeature_results.csv. 76 | In case user want to calculate all the features except AAI and ACR, the job name will be 'ALLCOMP'. Reason to leave AAI and ACR is, the feature calculation takes long time for longer sequences. 77 | 78 | Job name: It allows users to choose the type of composition, the user want to calculate, such as AAC which stands for Amino Acid composition. 79 | In case user do not provide any job name, it will choose AAC by default. 80 | 81 | N-terminal: It allows user to cut the specific number of residues from the N-terminal of the sequences. 82 | 83 | 84 | C-terminal: It allows user to cut the specific number of residues from the C-terminal of the sequences. 85 | 86 | NCT-terminal: It allows user to cut the specific number of residues from the N- and C-terminal of the sequences, and join them. 87 | 88 | Rest_N : It allow users to drop the specific number of residues from N-terminal, and perform operations on the rest. 89 | 90 | Rest_C : It allow users to drop the specific number of residues from C-terminal, and perform operations on the rest. 91 | 92 | Split: It allow users to divided the sequence into number of sequences. 93 | 94 | Lag : It defines the value for order of lag, lambda, gap or dipeptide, to calculate certain features. 95 | 96 | Weight: It defines the weight factor to calculate the quasi-sequence order, by default it is set at 0.1. 97 | 98 | Pweight: It defines the weight factor to calculate the pseudo and amphiphlic pseudo amino acid composition, by default it is set at 0.05. 99 | 100 | ############################################################################################################################################################################################################################# 101 | 102 | 2: Standalone for calculating binary profiles based features: 103 | 104 | **Important: To run this script 'Data' folder should be in the same directory.** 105 | 106 | Minimum USAGE: Minimum ussage is "pfeature_bin.py -i protein.fa" where protein.fa is a input fasta file. This will calculate the amino acid binary profile of the seqeunces provided in the fasta file. It will use other parameters by default. It will save output in "pfeature_result.csv" in CSV (comma seperated variables). 107 | 108 | usage: pfeature_bin.py [-h] -i INPUT [-o OUTPUT] 109 | [-j {AAB,DPB,ATB,BTB,PCB,AIB,ALLBIN}] [-n N_TERMINAL] 110 | [-c C_TERMINAL] [-nct NC_TERMINAL] [-rn REST_N] 111 | [-rc REST_C] [-s SPLIT] [-d LAG] 112 | 113 | Please provide following arguments 114 | 115 | optional arguments: 116 | -h, --help show this help message and exit 117 | -i INPUT, --input INPUT 118 | Input: protein or protein.sequence in FASTA format or single sequence per line in single letter code 119 | -o OUTPUT, --output OUTPUT 120 | Output: File for saving results by default pfeature_result.csv 121 | -j {AAB,DPB,ATB,BTB,PCB,AIB,ALLBIN}, --job {AAB,DPB,ATB,BTB,PCB,AIB,ALLBIN} 122 | Job Type: 123 | AAB: Amino acid based binary profile 124 | DPB: Dipeptide based binary profile 125 | ATB: Atom based binary profile 126 | BTB: Bond based binary profile 127 | PCB: Physico-chemical properties based binary profile 128 | AIB: Amino-acid indices based binary profile 129 | ALLBIN:All binary profiles together except ATB and BTB 130 | by default AAB 131 | -n N_TERMINAL, --n_terminal N_TERMINAL 132 | Window Length from N-terminal: by default 0 133 | -c C_TERMINAL, --c_terminal C_TERMINAL 134 | Window Length from C-terminal: by default 0 135 | -nct NC_TERMINAL, --nc_terminal NC_TERMINAL 136 | Residues from N- and C-terminal: by default 0 137 | -rn REST_N, --rest_n REST_N 138 | Number of residues removed from N-terminal, by default 0 139 | -rc REST_C, --rest_c REST_C 140 | Number of residues removed from C-terminal, by default 0 141 | -s SPLIT, --split SPLIT 142 | Number of splits a sequence divided into, by default 0 143 | -d LAG, --lag LAG This represents the order of gap, lag or dipeptide, by default 1 144 | 145 | #Parameters Description: 146 | 147 | Input File: It allow users to provide input in two format; 148 | i) FASTA format (standard) (e.g. protein.fa) 149 | ii) Simple Format, in this case, file should have sequences in a single line in single letter code (eg. protein.seq). 150 | 151 | Output File: Program will save result in CSV format, in the provided filename. 152 | In case user do not provide output file name, it will be stored in pfeature_results.csv. 153 | In case user want to calculate all the features except ATB and BTB, the job name will be 'ALLBIN'. Reason to leave ATB and BTB is, the number of atoms and bonds are not equal in all amino acid residues. 154 | 155 | Job name: It allows users to choose the type of composition, the user want to calculate, such as AAB which stands for Amino Acid based binary profile. 156 | In case user do not provide any job name, it will choose AAB by default. 157 | 158 | N-terminal: It allows user to cut the specific number of residues from the N-terminal of the sequences. 159 | 160 | 161 | C-terminal: It allows user to cut the specific number of residues from the C-terminal of the sequences. 162 | 163 | NCT-terminal: It allows user to cut the specific number of residues from the N- and C-terminal of the sequences, and join them. 164 | 165 | Rest_N : It allow users to drop the specific number of residues from N-terminal, and perform operations on the rest. 166 | 167 | Rest_C : It allow users to drop the specific number of residues from C-terminal, and perform operations on the rest. 168 | 169 | Split: It allow users to divided the sequence into number of sequences. 170 | 171 | Lag : It defines the value for order of dipeptide, to calculate the dipeptide based binary profiles. 172 | 173 | ############################################################################################################################################################################################################################# 174 | 175 | 3: Standalone for calculating PSSM profile 176 | 177 | **Important: To run this script a file with the file name 'envfile' is required.** 178 | 179 | *This envfile contains paths for the following scripts/data:* 180 | i) Path for blastpgp 181 | ii) Path for blast database 182 | iii) Path for makemat 183 | 184 | 185 | Minimum USAGE: Minimum ussage is "pfeature_pssm.py -i protein.fa" where protein.fa is a input fasta file. This will calculate the PSSM profile of the seqeunces provided in the fasta file. It will use other parameters by default. It will save output in "pssm_profile.csv" in CSV (comma seperated variables). 186 | 187 | -h, --help show this help message and exit 188 | -i INPUT, --input INPUT 189 | Input: protein or peptide sequence in FASTA format or single sequence per line in single letter code 190 | -o OUTPUT, --output OUTPUT 191 | Output: File for saving results by default pssm_profile.csv 192 | -n {N0,N1,N2,N3,N4}, --normalization_method {N0,N1,N2,N3,N4} 193 | Normalization Method: 194 | N0: It provides pssm profile without any normalization 195 | N1: It normalizes pssm profile based on 1/(1+e^-x) formula 196 | N2: It normalizes pssm profile based on (x-min)/(max-min) formula 197 | N3: It normalizes pssm profile based on ((x-min)/(max-min))*100 formula 198 | N4: It normalizes pssm profile based on 1/(1+e^-(x/100) formula 199 | By default it is N0 200 | 201 | #Parameters Description: 202 | 203 | Input File: It allow users to provide input in two format; 204 | i) FASTA format (standard) (e.g. protein.fa) 205 | ii) Simple Format, in this case, file should have sequences in a single line in single letter code (eg. protein.seq). 206 | 207 | Output File: Program will save result in CSV format, in the provided filename. 208 | In case user do not provide output file name, it will be stored in pssm_profile.csv 209 | 210 | Normalization methods: It allows user to normalize the PSSM profiles using four different formula. The description is as follows: 211 | N0: It provides pssm profile without any normalization 212 | N1: It normalizes pssm profile based on 1/(1+e^-x) formula 213 | N2: It normalizes pssm profile based on (x-min)/(max-min) formula 214 | N3: It normalizes pssm profile based on ((x-min)/(max-min))*100 formula 215 | N4: It normalizes pssm profile based on 1/(1+e^-(x/100) formula 216 | By default it is N0 217 | 218 | Pfeature Packakage Files 219 | ======================= 220 | It contantain following files, brief description of these files are given below: 221 | 222 | LICENSE : License information 223 | 224 | README.md : This file provide information about this package 225 | 226 | pfeature_comp.py : Python program to calculate composition based features 227 | 228 | pfeature_bin.py : Python program to calculate binary profile based features 229 | 230 | pfeature_pssm.py : Python program to calculate pssm profile based features 231 | 232 | protein.seq : Example file contain protein sequences in simple format 233 | 234 | protein.fa : Example file contain protein sequences in FASTA format 235 | 236 | Data : This folder contains the files required to calcuate the composition and binary profile based features. 237 | 238 | envfile : This file contains the path information required to run the pfeature_pssm.py script. 239 | 240 | Pfeature_Descriptors.pdf : This file comprises of description of the header of output files, which is generated using the aforementioned scripts. 241 | 242 | Requirement.txt : This file consists of commands and pre-requisite to run the aforementioned scripts. 243 | -------------------------------------------------------------------------------- /Standalone/Requirement.txt: -------------------------------------------------------------------------------- 1 | 1. Pre-requisite 2 | ========== 3 | In order to run this program user should have Python3, and scikit-learn library. 4 | 5 | 2. Command line 6 | ================ 7 | In order to know the arguments of any script, please run the following command: 8 | i. For Composition based features 9 | python pfeature_comp.py -h 10 | i. For Binary profile based features 11 | python pfeature_bin.py -h 12 | i. For PSSM profile based features 13 | python pfeature_pssm.py -h 14 | -------------------------------------------------------------------------------- /Standalone/Screenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raghavagps/Pfeature/1117d4c9712a7d230ed0e0026be8d9a2d859e978/Standalone/Screenshot.png -------------------------------------------------------------------------------- /Standalone/envfile: -------------------------------------------------------------------------------- 1 | #Path information for the generation of PSSM profile 2 | #User can change the paths according to their machines 3 | BLASTPGP:/home/gpsr/software/blastpr/blastpgp 4 | BLAST database:/usr1/software/blastpr/data/swissprot 5 | MAKEMAT:/home/gpsr/software/blastpr/makemat 6 | -------------------------------------------------------------------------------- /Standalone/pfeature_pssm.py: -------------------------------------------------------------------------------- 1 | import io 2 | import os 3 | import shlex 4 | import subprocess 5 | import glob 6 | import pandas as pd 7 | import numpy as np 8 | import sys 9 | import uuid 10 | import re 11 | import argparse 12 | from argparse import RawTextHelpFormatter 13 | parser = argparse.ArgumentParser(description='Please provide following arguments',formatter_class=RawTextHelpFormatter) 14 | parser.add_argument("-i","-I","--input", type=str, required=True, help="Input: protein or peptide sequence in FASTA format or single sequence per line in single letter code") 15 | parser.add_argument("-o","-O","--output",type=str, help="Output: File for saving results by default pssm_profile.csv") 16 | parser.add_argument("-n","-N","--normalization_method",type=str.upper, choices = ['N0','N1','N2','N3','N4'], help="Normalization Method:\nN0: It provides pssm profile without any normalization\nN1: It normalizes pssm profile based on 1/(1+e^-x) formula\nN2: It normalizes pssm profile based on (x-min)/(max-min) formula\nN3: It normalizes pssm profile based on ((x-min)/(max-min))*100 formula\nN4: It normalizes pssm profile based on 1/(1+e^-(x/100) formula\nBy default it is N0") 17 | args = parser.parse_args() 18 | 19 | # Input variable 20 | sequencefile= args.input 21 | # Output file 22 | if args.output == None: 23 | result_filename= "pssm_profile.csv" 24 | else: 25 | result_filename = args.output 26 | if args.normalization_method == None: 27 | nm= "N0" 28 | else: 29 | nm = args.normalization_method 30 | 31 | def pssm_2(file): 32 | pd.options.display.float_format = '{:.2e}'.format 33 | df=file 34 | df1 = df 35 | df2 = df1.applymap(pssm_1) 36 | return df2 37 | def pssm_1(x): 38 | if nm == 'N0': 39 | if type(x) is str: 40 | return x 41 | elif x: 42 | return x 43 | else: 44 | return 45 | if nm == 'N1': 46 | if type(x) is str: 47 | return x 48 | elif x < -700: 49 | return 0 50 | elif x: 51 | return (1/(1+(2.7182)**(-x))) 52 | else: 53 | return x 54 | if nm == 'N2': 55 | a = 1000 56 | b = -1000 57 | if type(x) is str: 58 | return x 59 | elif x: 60 | return (x-a)/(b - a) 61 | else: 62 | return 63 | if nm == 'N3': 64 | a = 1000 65 | b = -1000 66 | if type(x) is str: 67 | return x 68 | elif x: 69 | return ((x-a)*100)/(b - a) 70 | else: 71 | return 72 | if nm == 'N4': 73 | if type(x) is str: 74 | return x 75 | elif x: 76 | return (1/(1+(2.7182)**(-x/100))) 77 | else: 78 | return 79 | def readseq(file,out): 80 | with open(file) as f: 81 | records = f.read() 82 | records = records.split('>')[1:] 83 | seqid = [] 84 | seq = [] 85 | for fasta in records: 86 | array = fasta.split('\n') 87 | name, sequence = array[0].split()[0], re.sub('[^ARNDCQEGHILKMFPSTWYV-]', '', ''.join(array[1:]).upper()) 88 | seqid.append(name) 89 | seq.append(sequence) 90 | if len(seqid) == 0: 91 | f=open(file,"r") 92 | data1 = f.readlines() 93 | for each in data1: 94 | seq.append(each.replace('\n','')) 95 | for i in range (1,len(seq)+1): 96 | seqid.append("Seq_"+str(i)) 97 | for i in seq: 98 | if 'B' in i: 99 | print('\nError: The input sequences contain non-natural amino acids. Kindly check the sequence.\n') 100 | sys.exit() 101 | if 'J' in i: 102 | print('\nError: The input sequences contain non-natural amino acids. Kindly check the sequence.\n') 103 | sys.exit() 104 | if 'O' in i: 105 | print('\nError: The input sequences contain non-natural amino acids. Kindly check the sequence.\n') 106 | sys.exit() 107 | if 'U' in i: 108 | print('\nError: The input sequences contain non-natural amino acids. Kindly check the sequence.\n') 109 | sys.exit() 110 | if 'Z' in i: 111 | print('\nError: The input sequences contain non-natural amino acids. Kindly check the sequence.\n') 112 | sys.exit() 113 | if 'X' in i: 114 | print('\nError: The input sequences contain non-natural amino acids. Kindly check the sequence.\n') 115 | sys.exit() 116 | df4 = pd.DataFrame(seq) 117 | df4.to_csv(out,index=None,header=False) 118 | def pssm(inputfile,outputfile): 119 | if os.path.exists('envfile'): 120 | with open('envfile', 'r') as file: 121 | data = file.readlines() 122 | output = [] 123 | for line in data: 124 | if not "#" in line: 125 | output.append(line) 126 | if len(output)==3: 127 | paths = [] 128 | for i in range (0,len(output)): 129 | paths.append(output[i].split(':')[1].replace('\n','')) 130 | blastpgp = paths[0] 131 | blastdb = paths[1] 132 | makemat = paths[2] 133 | if os.path.isfile(blastpgp) and os.access(blastpgp, os.R_OK): 134 | print('The provided directory for blastpgp is correct and readable.') 135 | else: 136 | print("########################################################################################################################") 137 | print("Error: Either 'blastbgp' file is missing from the provided directory in the 'envfile', or not readable. Kindly check.", file=sys.stderr) 138 | print("########################################################################################################################") 139 | sys.exit() 140 | if os.path.isfile(makemat) and os.access(makemat, os.R_OK): 141 | print('The provided directory for makemat is correct and readable.') 142 | else: 143 | print("########################################################################################################################") 144 | print("Error: Either 'makemat' file is missing from the provided directory in the 'envfile', or not readable. Kindly check.", file=sys.stderr) 145 | print("########################################################################################################################") 146 | sys.exit() 147 | if (glob.glob(blastdb+".pin")) and (glob.glob(blastdb+".psq")) and (glob.glob(blastdb+".phr")): 148 | print('The provided directory for blast database is correct and readable.') 149 | else: 150 | dbfiles = blastdb.split('/')[-1] 151 | print("##############################################################################################################################################################################################") 152 | print("Error: Either the files for BLAST database are missing from the provided directory in the 'envfile', or not readable. Please provide the files with extension of", dbfiles+".pin,", dbfiles+".phr,", dbfiles+".psq in the provided directory.", "Kindly check.", file=sys.stderr) 153 | print("##############################################################################################################################################################################################") 154 | sys.exit() 155 | 156 | else: 157 | print("####################################################################################") 158 | print("Error: Please provide the '{}', which comprises paths for BLASTPGP and MAKEMAT".format('envfile'), file=sys.stderr) 159 | print("####################################################################################") 160 | sys.exit() 161 | ss = [] 162 | file_list = [] 163 | readseq(inputfile,'temp.readseq') 164 | df1 = pd.read_csv('temp.readseq', header=None) 165 | aa = [] 166 | for i in df1[0]: 167 | aa.append(len(i)) 168 | for i in range(0,len(df1)): 169 | ss.append('>seq_'+str(i+1)) 170 | df1['seq'] = ss 171 | df1 = df1[['seq',0]] 172 | for ii in range(0,len(df1)): 173 | name_file = df1['seq'][ii].replace('>','')+'.fasta' 174 | file_out = df1['seq'][ii].replace('>','')+'.pssmout' 175 | file_list.append(df1['seq'][ii].replace('>','')+'.mtx') 176 | df1.iloc[ii].to_csv(name_file, index=None, header=False, sep='\n') 177 | filename, file_extension = os.path.splitext(name_file) 178 | filename_o, file_extension_o = os.path.splitext(file_out) 179 | S = blastpgp + ' -d ' + blastdb + ' -i ' + name_file + ' -j 3 -C ' + file_out 180 | os.system(S) 181 | os.rename(file_out, filename_o + '.chk') 182 | outputfile1 = filename_o + ".chk" 183 | temp1 =filename_o + ".sn" 184 | C2 = 'echo {} > {}'.format(name_file,temp1) 185 | os.system(C2) 186 | temp2 = filename_o + ".pn" 187 | C1 = 'echo {} > {}'.format(outputfile1,temp2) 188 | os.system(C1) 189 | P = makemat + ' -P ' + filename_o 190 | os.system(P) 191 | dir = '.' 192 | tt = [] 193 | for i in file_list: 194 | ss = [] 195 | fp = open(i) 196 | all_line = fp.readlines() 197 | ss.append(all_line[14:]) 198 | uu = [] 199 | for j in all_line[14:]: 200 | uu.append(j.replace('\n','').replace(' ',',')) 201 | np.savetxt(i+'_temp',uu, fmt="%s") 202 | df11 = pd.read_csv(i+'_temp', header=None, sep=",") 203 | col = [1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,22] 204 | df13 = df11.iloc[:,col].reset_index(drop=True) 205 | df12 = pssm_2(df13) 206 | for i in range(0,len(df12)): 207 | tt.extend(df12.loc[i]) 208 | bb = [] 209 | cc = 0 210 | for i in range(0,len(aa)): 211 | bb.append(tt[cc:cc+20*(aa[i])]) 212 | cc = cc+20*(aa[i]) 213 | df123 = pd.DataFrame(bb) 214 | df456 = df123.fillna('NA') 215 | df456.to_csv(outputfile,index=None,header=False,float_format='%.2e') 216 | allfiles = os.listdir(dir) 217 | for item in allfiles : 218 | if item.endswith(".aux") or item.endswith(".sn") or item.endswith(".pn") or item.endswith(".mn") or item.endswith(".mtx_temp") or item.endswith(".mtx") or item.endswith(".chk") or item.endswith(".fasta") or item.endswith(".readseq"): 219 | os.remove(os.path.join(dir, item)) 220 | 221 | pssm(sequencefile,result_filename) 222 | -------------------------------------------------------------------------------- /Standalone/pfeature_standalone.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raghavagps/Pfeature/1117d4c9712a7d230ed0e0026be8d9a2d859e978/Standalone/pfeature_standalone.zip -------------------------------------------------------------------------------- /Standalone/protein.fa: -------------------------------------------------------------------------------- 1 | >Seq_1 2 | PAAAAQAVAGLAPVAAEQMALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN 3 | >Seq_2 4 | MMFRSVIPVLLFLIPLLLSAQAANSLRACGPALMDMLRVACPNGFNSMFAKRGTLGLFDYEDHLADLDSSESHHMNSLSSIRRDFRGVVDSCCRKSCSFSTLRAYCDS 5 | >Seq_3 6 | MALWTRLLPLLALLALWAPAPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREAENPQAGAVELGGGLGGLQALALEGPPQKRGIVEQCCTSICSLYQLENYCN 7 | -------------------------------------------------------------------------------- /Standalone/protein.seq: -------------------------------------------------------------------------------- 1 | PAAAAQAVAGLAPVAAEQMALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN 2 | MMFRSVIPVLLFLIPLLLSAQAANSLRACGPALMDMLRVACPNGFNSMFAKRGTLGLFDYEDHLADLDSSESHHMNSLSSIRRDFRGVVDSCCRKSCSFSTLRAYCDS 3 | MALWTRLLPLLALLALWAPAPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREAENPQAGAVELGGGLGGLQALALEGPPQKRGIVEQCCTSICSLYQLENYCN 4 | -------------------------------------------------------------------------------- /scripts/Pfeature_scripts.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raghavagps/Pfeature/1117d4c9712a7d230ed0e0026be8d9a2d859e978/scripts/Pfeature_scripts.zip -------------------------------------------------------------------------------- /scripts/readme: -------------------------------------------------------------------------------- 1 | ## Python scripts in python, these scripts can run independently 2 | --------------------------------------------------------------------------------