[Biopython] NCBIWWW.qblast() - 'max matches in query range'?

[Peter Cock]

Using the command line BLAST+ tools is probably best,
unless the QBLAST API has been updated and adds
this functionality and we just hadn't noticed?

Peter


On Thu, May 10, 2018 at 7:21 PM, Schiraldi, Nicholas J <
nschiraldi at albany.edu> wrote:

> Hi,
>
>
>
> Full disclosure – I’m not a biologist, but helping a biology lab
> streamline some of their bioinformatics. Through NCBIWWW, I’d like to run a
> blastx with the website equivalent of ‘max matches in query range’. There
> doesn’t appear to be a keyword applicable through the web API for this
> limitation. I found this post from over a year ago, but wasn’t sure if this
> feature has since been supported: https://www.biostars.org/p/213407/
>
>
>
> Should I instead turn to the command line tools as suggested in the thread?
>
>
>
> Thanks for your help,
>
>
>
> Nick
>
>
>
> # SAMPLE CODE #
>
> from Bio.Blast import NCBIWWW
>
> from Bio import SeqIO
>
>
>
> blastx = NCBIWWW.qblast(
>
>     program='blastx',
>
>     database='nr',
>
>     sequence=[sequence],
>
>     gapcosts='9 1',
>
>     matrix_name='BLOSUM62',
>
> )
>
>
>
>
>
>
>
> *Nicholas Schiraldi, Ph.D.*
>
> Data Analytics and Visualization Specialist
>
> Academic and Research Computing Center, ITS
>
> University at Albany
>
>
>
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>
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