<div dir="ltr">Using the command line BLAST+ tools is probably best,<div>unless the QBLAST API has been updated and adds</div><div>this functionality and we just hadn't noticed?</div><div><br></div><div>Peter</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, May 10, 2018 at 7:21 PM, Schiraldi, Nicholas J <span dir="ltr"><<a href="mailto:nschiraldi@albany.edu" target="_blank">nschiraldi@albany.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal">Hi,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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:
<a href="https://www.biostars.org/p/213407/" target="_blank">https://www.biostars.org/p/<wbr>213407/</a>
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Should I instead turn to the command line tools as suggested in the thread?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thanks for your help,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Nick<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"># SAMPLE CODE #<u></u><u></u></p>
<p class="MsoNormal">from Bio.Blast import NCBIWWW<u></u><u></u></p>
<p class="MsoNormal">from Bio import SeqIO<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">blastx = NCBIWWW.qblast(<u></u><u></u></p>
<p class="MsoNormal"> program='blastx',<u></u><u></u></p>
<p class="MsoNormal"> database='nr',<u></u><u></u></p>
<p class="MsoNormal"> sequence=[sequence],<u></u><u></u></p>
<p class="MsoNormal"> gapcosts='9 1',<u></u><u></u></p>
<p class="MsoNormal"> matrix_name='BLOSUM62',<u></u><u></u></p>
<p class="MsoNormal">)<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><b>Nicholas Schiraldi, Ph.D.<u></u><u></u></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#3b3838">Data Analytics and Visualization Specialist<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#3b3838">Academic and Research Computing Center, ITS<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#3b3838">University at Albany<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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