[Biopython-dev] Parsing RPS-Blast output with BioPython

Peter biopython-dev at maubp.freeserve.co.uk
Mon Dec 6 14:42:11 EST 2004

Has anyone looked at using BioPython with the NCBI's (standalone) 
RPS-Blast program?

RPSBLAST = Reverse Position Specific BLAST, used to query a protein 
sequence against the Conserved Domain Database, Pfam, SMART etc.

I've had a little look at the NCBIStandalone.py, and can see how a 
function rpsblast could be added, based on the existing blastall or 
blastpgp functions.

(i.e. Make a copy of blastpgp and called it rpsblast)

However, it would appear that the output parser will need some 
additional work to understand the RPS-BLAST output...


MOAC Doctoral Training Centre
University of Warwick, UK

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