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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Hi Peter,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Thanks for the reply. The confusing thing is that Bio.Blast.NCBIWWW.qblast() does return the same result as the NCBI BLAST website. So my query is more a blast one rather
than a biopython one but I couldn’t think of a better place to ask this query.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">My fasta file contains a gene called
</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">Listeria monocytogenes EGD-e chromosome with gi|16802048:2172068-2173591.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">Just to verify that this is what it says it is and for my own curiosity, I uploaded the entire fasta file to the NCBI BLAST website and, as expected, it returns
that this is indeed Listeria monocytogenes EGD-e chromosome with gi|16802048:2172068-2173591.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">However if I open the fasta file, copy the sequence
<u>only</u> out of the file and paste into NCBI BLAST, I get a result of Listeria monocytogenes WSLC1001 complete genome with gi|584465821|gb|CP007160 (same as my biopython result). I’m trying to understand why the correct gene isn’t identified using just the
sequence. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">Thanks again,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">Aisling.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Aisling O'Driscoll
<br>
<b>Sent:</b> 13 November 2014 21:32<br>
<b>To:</b> biopython@biopython.org<br>
<b>Subject:</b> Blast query<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Hi,<br>
<br>
I have a query re BLAST output. I have written a BioPython script that takes the attached betl gene sequence and runs a blast. It returns results for Listeria monocytogenes WSLC1001 complete genome with gi|584465821|gb|CP007160.1.<br>
<br>
I run the same from the NCBI web interface just to verify the output and it also returns this result.
<br>
<br>
However why is it that it does not return the correct match of Listeria monocytogenes EGD-e chromosome with gi|16802048:2172068-2173591 as we can see at the top of the attached fasta file?<br>
<br>
Thanks in advance<br>
Aisling.<o:p></o:p></span></p>
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