MSBlast

Category(ies): Bioinformatics

Version: 2003

a specialised BLAST –based protocol developed for identification of proteins by sequence similarity searches using peptide sequences produced by the interpretation of tandem mass spectra. MS BLAST is described in detail in: Shevchenko, A., Sunyaev, S., Loboda, A., Shevchenko, A., Bork, P., Ens, W., and Standing, K. (2001). Charting the proteomes of organisms with unsequenced genomes by MALDI- Quadrupole Time-of-Flight mass spectrometry and BLAST homology searching, Anal Chem 73, 1917-1926.

altix: Not available on altix

pcluster: Not available on pcluster

rcluster,IOB: running program | Documentation | Installation | System

Running Program: also refer to submit jobs to queues at rcluster,IOB

e.g.

run_msblast.pl -db /db/wublast/nrdb95 -query example1.seq -uniq_pep 5 -output test3 -wudir /usr/local/wublast/

Sample of sub.sh

#!/bin/csh
cd working_directory
time run_msblast.pl -db /db/wublast/nrdb95 < -query example1.seq -uniq_pep 5 -output test3 -wudir /usr/local/wublast/ >myout

bsub -q r1-24h -o test.%J.out -e test.%J.err ./sub.sh

Documentation: Online document available at MSBlast website

Installation: source downloaded from MSBlast website.

System(s): Unix