Program: PICSI Description: Proteomics Identification from Cross-Species Inference Version: 1.2 Last Edit: 26/03/14 Citation: Jones, Edwards et al. (2011), Marine Biotechnology 13(3): 496-504.

Copyright © 2010 Richard J. Edwards - See source code for GNU License Notice

Imported modules: budapest rje rje_seq rje_zen rje_blast_V2

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

Function

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

Commandline

### ~~~ INPUT OPTIONS ~~~ ###
seqin=FILE : File containing sequences hit during searches [None]
resfiles=FILES : List of CSV MASCOT output files []
sumfile=FILE : Delimited summary file containing search,prot_hit_num,prot_acc,prot_desc,pep_seq
qryspec=FILE : Species code for Query species [EMIHU]
spectdt=FILE : File of UniProt species translations ['/scratch/RJE_Filestore/SBSBINF/Databases/DBase_090505/UniProt/uniprot.spec.tdt']
### ~~~ OUTPUT OPTIONS ~~~ ###
basefile=FILE : Base for output files [picsi]
delimit=X : Delimiter for output files [tab]

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.