Module: rje_phos Description: RJE Phosphorylation Module Version: 0.1 Last Edit: 26/10/07

Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_seq rje_uniprot rje_zen rje_blast_V1

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module is for the control and management of different phosphorylation sources and for mapping known phosphosites onto other proteins. Initially, the reading and processing of PhosphoELM is the only source implemented, although phosphorylation prediction may be added with time.

The phosBLAST method will take an input dataset and BLAST them against the phosphorylation database(s), align hits above a certain GABLAM %ID and mark the phosphosites on the sequence. A second %ID cut-off will be used to determine which sites are marked as identities and which as homologies. Outputs will include an alignment with all the phosphoHomologues plus a simpler "alignment" of the query protein and marked sites. Phosphorylation predictions may be added to this second simpler "alignment". A UniProt-format file could also be produced with phosphoSites marked.

Commandline

PhosphoELM Input Options (Creates Fasta file if pELM given)

pelm=FILE : Filename for phosphoELM download [None]
filterseq=T/F : Apply rje_seq sequence filters to phosphoELM data [False]
pelmfas=FILE : Filename for fasta file output of pELM sequences [pelm.fas]

PhosBLAST Options

phosblast=FILE : Fasta file of sequences to perform phosBLAST method against pELM [None]
usespec=T/F : Use species codes for determing same species for ID matches [True]
idsim=X : Percentage identity (GABLAM; phosblast qry) for marking as identity [95.0]
homsim=X : Percentage identity (GABLAM; phosblast qry) for marking as homologue [40.0]
phosdat=T/F : Whether to produce a modified UniProt-format file with potential phosphoSites as features [False]
phosres=FILE : Delimited text file containing input sequence, position and evidence [*.phosres.tdt]

History Module Version History

    # 0.0 - Initial Compilation. Basic pELM parsing done.
    # 0.1 - Added phosBLAST method.