[Bioperl-l] Bio::Index::Blast bug

Peter biopython at maubp.freeserve.co.uk
Wed Mar 10 05:35:56 EST 2010

On Wed, Mar 10, 2010 at 8:20 AM, Till Bayer <till.bayer at kaust.edu.sa> wrote:
> Hi all!
> I tried to use Bio::Index::Blast, but always got the first hit back, no
> matter what ID I used. The reason is that the Blast indexer seems to use
> 'BLAST' as a record separator in all cases, except for RPS-BLAST.
> I think however that for the current versions of blastall and blast+
> 'Query=' should be used.

That fits with changes I had to make in Biopython for breaking
up the plain text BLAST output into each query. For a while only
the RPS-BLAST report omitted the "header" (the BLAST line
and the journal references users should cite) between records,
but now all the NCBI BLAST tools do this - forcing us to look
for the Query= line.

i.e. I can't comment on the BioPerl change itself, but your
reasoning about the BLAST output makes sense.


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