APORC Document Center: PTMPred

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PTMPred: a toolbox for predicting post-transcriptional modification sites from protein sequences

Manual#

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.

Phospredictor#

Data File#

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#

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#

Phospredictor <Kinase name> <Input File> <C> <Cutoff>

where <Kinase name> is Kinase name such as "PKA", <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:

Phospredictor  PKA  uniprot.fasta  0.0005  0.5

OGlypredictor#

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 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

Software and Data#

Contacts#

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

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