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| __PTMPred__: a toolbox for predicting post-transcriptional modification sites from protein sequences |
| __PTMPred__: A tool for predicting post-transcriptional modification sites from protein sequences |
| * Last updated: May 28, 2010 |
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| PTMpred is a toolbox for predicting post-transcriptional modification sites based on protein sequence. Currently there are two programs: one for phosphorylation sites, the other for O-glycosylation sites. The programs are implemented in C. The win32 console version is provided. |
| PTMpred is a tool for predicting post-transcriptional modification sites based on protein sequence. The program is implemented in C. The win32 console version and linux version are provided. |
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| !!Phospredictor |
| !!Training Data File |
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| !Data File |
| The "*_Pos.txt" and "*_Neg.txt" are the positive and negative training sequence fragments respectively, where * represents the PTM type such as "PKA" or "OGly". The user can replace these files by their own training data. |
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| The "*_Pos.txt" and "*_Neg.txt" are the positive and negative training sequence fragments respectively. The user can replace these files by theri own training data. |
| !!Input File |
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| !Input File |
|
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| !Command Line |
| !!Command Line |
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| Phospredictor <Kinase name> <Input File> <C> <Cutoff> |
| PTMpred <PTM Type> <Input File> <C> <Cutoff> |
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| where <Kinase name> is Kinase name such as "PKA", <Input File> are specified above, and <C> <Cutoff> is the paramters. |
| where <PTM Type> is PTM type such as "PKA" or "OGly" used in the filename of training data, and <C> <Cutoff> are the parameters. The parameter C can be any positive real number between 0.00005 and 0.5. The Cutoff should be real number between 0 and 1. |
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| The paramter C can be any positive real number between 0.00005 and 0.5. The Cutoff should be real number between 0 and 1. |
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| Phospredictor PKA uniprot.fasta 0.0005 0.5 |
| PTMpred PKA uniprot.fasta 0.0005 0.5 |
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| !!OGlypredictor |
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| !Data File |
|
| The "OGly_Pos.txt" and "OGly_Neg.txt" are the positive and negative training sequence fragments respectively. The user can replace these files by theri own training data. |
|
| !Input File |
|
| The input file is in the FASTA format. Each file can includes one or multiple sequences. Each sequence must have the amino acid "S" or "T". More sequences require more computer resource. For typical computer, the number of sequences less than 50 should be fine. |
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| The output will be saved into "Result.txt" in the same directory. |
|
| !Command Line |
|
| {{{ |
| OGlypredictor <Input File> <C> <Cutoff> |
| }}} |
| where <Input File> are specified above, and <C> <Cutoff> is the paramters. |
|
| The paramter C can be any positive real number between 0.00005 and 0.5. The Cutoff should be real number between 0 and 1. |
|
| For examle: |
| {{{ |
| OGlypredictor uniprot.fasta 0.0005 0.1 |
| }}} |
|
|
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| * [Phospredictor.rar|File:PTMPred/Phospredictor.rar] |
| * [OGlypredictor.rar|File:PTMPred/OGlypredictor.rar] |
| * Note: This software is still under development and the new version will be released soon. (May 28, 2010) |
| * [PTMPred.rar|PTMPred/PTMPred.rar] |
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