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

[Schiraldi, Nicholas J]

Thanks, I don’t see an obvious answer in the QBLAST API … so probably not.

From: Peter Cock <p.j.a.cock at googlemail.com>
Sent: Thursday, May 10, 2018 5:30 PM
To: Schiraldi, Nicholas J <nschiraldi at albany.edu>
Cc: biopython at mailman.open-bio.org
Subject: Re: [Biopython] NCBIWWW.qblast() - 'max matches in query range'?

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<mailto: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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