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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></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/">https://www.biostars.org/p/213407/</a>
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Should I instead turn to the command line tools as suggested in the thread?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for your help,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Nick<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"># SAMPLE CODE #<o:p></o:p></p>
<p class="MsoNormal">from Bio.Blast import NCBIWWW<o:p></o:p></p>
<p class="MsoNormal">from Bio import SeqIO<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">blastx = NCBIWWW.qblast(<o:p></o:p></p>
<p class="MsoNormal"> program='blastx',<o:p></o:p></p>
<p class="MsoNormal"> database='nr',<o:p></o:p></p>
<p class="MsoNormal"> sequence=[sequence],<o:p></o:p></p>
<p class="MsoNormal"> gapcosts='9 1',<o:p></o:p></p>
<p class="MsoNormal"> matrix_name='BLOSUM62',<o:p></o:p></p>
<p class="MsoNormal">)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b>Nicholas Schiraldi, Ph.D.<o:p></o:p></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#3B3838">Data Analytics and Visualization Specialist<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#3B3838">Academic and Research Computing Center, ITS<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#3B3838">University at Albany<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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