[Biopython-dev] Using BLAST et al with multiple queries

Peter biopython-dev at maubp.freeserve.co.uk
Mon Dec 13 15:28:16 EST 2004

Peter wrote:
> In short: does anyone else use FASTA files containing multiple
> sequences as input queries to standalone Blast?  How do you parse the
> output?

Ahem.  The answer is to use the NCBIStandalone.Iterator, which does 
appear to work as expected for blastp at least.  It doesn't (yet) work 
for RPS-BLAST output (see previous email), and I am looking at that.

I don't know how I missed this this object... its even in the cookbook:

3.1.6  Parsing a file full of BLAST runs


PhD Student
MOAC Doctoral Training Centre
University of Warwick, UK

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