[Biopython] Blast query

[Aisling O'Driscoll]

Hi Peter,

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.

My fasta file contains a gene called Listeria monocytogenes EGD-e chromosome with gi|16802048:2172068-2173591.
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.

However if I open the fasta file, copy the sequence only 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.

Thanks again,
Aisling.

From: Aisling O'Driscoll
Sent: 13 November 2014 21:32
To: biopython at biopython.org
Subject: Blast query

Hi,

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.

I run the same from the NCBI web interface just to verify the output and it also returns this result.

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?

Thanks in advance
Aisling.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20141114/140d2619/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: betl.fasta
Type: application/octet-stream
Size: 1633 bytes
Desc: betl.fasta
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20141114/140d2619/attachment-0001.obj>