[Biopython] Blast query

[Peter Cock]

Hi Aisling,

We have an FAQ in the Tutorial which is probably the answer here:

Q: Why doesn’t Bio.Blast.NCBIWWW.qblast() give the same results as the
NCBI BLAST website?
A: You need to specify the same options – the NCBI often adjust the
default settings on the website, and they do not match the QBLAST
defaults anymore. Check things like the gap penalties and expectation
threshold.

http://biopython.org/DIST/docs/tutorial/Tutorial.html

Peter


On Fri, Nov 14, 2014 at 6:32 AM, Aisling O'Driscoll
<Aisling.ODriscoll at cit.ie> wrote:
> 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.
>
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