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https://github.com/baderlab/powclui
POW! PDZ domain-peptide interaction prediction command line user interface
https://github.com/baderlab/powclui
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POW! PDZ domain-peptide interaction prediction command line user interface
- Host: GitHub
- URL: https://github.com/baderlab/powclui
- Owner: BaderLab
- License: lgpl-3.0
- Created: 2018-11-06T01:49:16.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2018-11-06T02:00:51.000Z (about 6 years ago)
- Last Synced: 2024-11-05T10:26:06.040Z (about 2 months ago)
- Language: Java
- Size: 14.7 MB
- Stars: 0
- Watchers: 12
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: Readme.txt
Awesome Lists containing this project
README
README
======
POWSeqCLUI (POW Seq Command Line User Interface)
POWStructCLUI (POW Struct Command Line User Interface)
April 10, 2013
Authors: Shirley Hui, Gary D. Bader
University of Toronto, Dept. Molecular Genetics
Please cite:
Hui S, Bader GD, BMC Bioinformatics 2010, 11:507
Hui S, Xing X, Bader GD, BMC Bioinformatics 2013, 14:27
Software is distribued AS IS under the GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007
Website version: http://webservice.baderlab.org/domains/POW/
REQUIREMENTS
============
This software is a java application and is confirmed to run under Java version 1.5.0_30.
HOW TO RUN
==========
1) Unzip POWCLUI.zip in a directory
2) At the command line, run one of the following commands in the directory above.
POWSeqCLUI:
java -cp .:lib/libsvm-2.89-pdzsvm.jar org.baderlab.pdzsvm.analysis.POWSeqCLUI
POWStructCLUI:
java -cp .:lib/libsvm-2.89-pdzsvm.jar org.baderlab.pdzsvm.analysis.POWStructCLUI
Parameters:
: H = Human, M = Mouse, W = Worm, F = Fly
: Path to a file containing the PDZ domain names (one per line)
: Path to a file containing the peptides of length five (one per line)
Note: POWCLUI takes exactly three parameters.
OUTPUT
======
Domain names that are repeated or not supported are skipped.
Peptides that are too short (< 5), contain invalid residues or are repeated are skipped.
Peptides that are too long (> 5) are truncated and skipped if repeated.
The programs will output information for all predictions (positive and negative).
Information reported include:
* Domain Name
* Binding Site Sequence (POWSeqCLUI only)
* Peptide Sequence
* Decision Value
EXAMPLES
========
1) POWSeqCLUI Output:
>java -cp .:lib/libsvm-2.89-pdzsvm.jar org.baderlab.pdzsvm.analysis.POWSeqCLUI H examples/PDZDomains.txt examples/Peptides.txt
POWSeqCLUI (POW Seq Command Line User Interface)
April 10, 2013
Authors: Shirley Hui, Gary D. Bader
University of Toronto, Dept. Molecular Genetics
Please cite:
Hui S, Bader GD, BMC Bioinformatics 2010, 11:507
Hui S, Xing X, Bader GD, BMC Bioinformatics 2013, 14:27
Software is distribued AS IS under the GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007
Organism: H
Domain Names:
Error: Domain BLAH not supported, skipping...
2 domain(s) read...
Peptides:
Warning: Peptide EDTWV already in list, skipping...
Error: Peptide S too short, skipping...
Warning: Peptide SSEDTWV too long, truncating...
Warning: Peptide EDTWV already in list, skipping...
Error: Invalid residue in peptide 12345, skipping...
3 peptide(s) read...
Results:
DomainName BindingSiteSequence PeptideSequence DecisionScore
DLG1-1 GLGFSIAGTKIGHSVA FLGWF -1.8040996291275562
DLG1-1 GLGFSIAGTKIGHSVA EDTWV -0.19450785721099295
DLG1-1 GLGFSIAGTKIGHSVA SSSSS -1.3645443983035186
MPDZ-1 SLGFSVVGQEQSHQIA FLGWF 0.6199364236346863
MPDZ-1 SLGFSVVGQEQSHQIA EDTWV 0.5265758575783792
MPDZ-1 SLGFSVVGQEQSHQIA SSSSS -1.3837781314980506
1) POWStructCLUI Output:
>java -cp .:lib/libsvm-2.89-pdzsvm.jar org.baderlab.pdzsvm.analysis.POWStructCLUI H examples/PDZDomains.txt examples/Peptides.txt
POWStructCLUI (POW Struct Command Line User Interface)
April 10, 2013
Authors: Shirley Hui, Gary D. Bader
University of Toronto, Dept. Molecular Genetics
Please cite:
Hui S, Bader GD, BMC Bioinformatics 2010, 11:507
Hui S, Xing X, Bader GD, BMC Bioinformatics 2013, 14:27
Software is distribued AS IS under the GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007
Organism: H
Domain Names:
Error: Domain BLAH not supported, skipping...
2 domain(s) read...
Peptides:
Warning: Peptide EDTWV already in list, skipping...
Error: Peptide S too short, skipping...
Warning: Peptide SSEDTWV too long, truncating...
Warning: Peptide EDTWV already in list, skipping...
Error: Invalid residue in peptide 12345, skipping...
3 peptide(s) read...
Results:
DomainName PeptideSequence DecisionScore
MPDZ-1 FLGWF 1.3722791766167184
MPDZ-1 SSSSS -2.298175924389645
MPDZ-1 EDTWV 0.6017692863722264
DLG1-1 FLGWF -1.214349274364786
DLG1-1 SSSSS -2.5483924802411475
DLG1-1 EDTWV 0.9241258336582265