RJE Phosphorylation Module
Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice
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.
PhosphoELM Input Options (Creates Fasta file if pELM given)
History Module Version History
# 0.0 - Initial Compilation. Basic pELM parsing done. # 0.1 - Added phosBLAST method.
© 2015 RJ Edwards. Contact: firstname.lastname@example.org.