Proteomics Identification from Cross-Species Inference
Copyright © 2010 Richard J. Edwards - See source code for GNU License Notice
See SLiMSuite Blog for further documentation.
This module is for cross-species protein identifications using searches against NCBInr, for example. MASCOT processing uses BUDAPEST. Hits are then converted into peptides for redundancy removal. Hits from a given (known) query species are preferentially kept and any peptides belonging to those hits are purged from hits returned by other species. All hits are then classified: - UNIQUE : Contains 2+ peptides, including 1+ unique peptides - NR : Contains 2+ peptides; None unique but 1+ peptides only found in other "NR" proteins - REDUNDANT : Contains 2+ peptides but all found in proteins also containing UNIQUE peptides - REJECT : Identified by <2 peptides once query-species peptides subtracted
### ~~~ INPUT OPTIONS ~~~ ###
See also rje.py generic commandline options.
History Module Version History
# 0.0 - Initial Compilation. # 1.0 - Basic working version. # 1.1 - Updated to blast_V2 and BLAST+. # 1.2 - Updated to BUDAPEST 2.3 and rje_mascot.
© 2015 RJ Edwards. Contact: firstname.lastname@example.org.