PTMPred: A tool for predicting post-transcriptional modification sites from protein sequences

• Last updated: May 28, 2010

Manual#

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.

Training 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.

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.

The output will be saved into "Result.txt" in the same directory.

Command Line#

PTMpred <PTM Type> <Input File> <C> <Cutoff>

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.

For examle:

PTMpred  PKA  uniprot.fasta  0.0005  0.5

Software and Data#

• Note: This software is still under development and the new version will be released soon. (May 28, 2010)
• PTMPred.rar

Contacts#

Any question or advice please email to wangxiao_bo_happy@126.com

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Category: Software