[Biopython] align sequence to genomic DNA

[Horea Chrristian]

 Thanks for your answer. I want my code to be as reproducible as
possible and have as little dependencies as possible, so I would rather
use remote BLAST than set it up (and expect all my users to set it up)
locally. is there any way to BLAST remotely just against the mouse? You
said BLAST might not be the best solution - what then? I tried EMBOSS'
supermatcher, but that requires local sequences and is excruciatingly
slow.... 

Also, my main concern right now is finding the position of my hits on
the genome (chromosome) - could you also tell me something about that?

Best,
Christian

On Fre, 2015-02-27 at 21:43 +0000, Peter Cock wrote:

> On Fri, Feb 27, 2015 at 5:42 PM, Horea Chrristian <h.chr at mail.ru> wrote:
> > Hi again, I am trying to align a sequence to the mouse genome,
> > I am currently doing it thus ... [BLAST against nt database].
> 
> BLAST may not be the best tool for this (depending on how
> many and how long your sequences are it could be fine).
> 
> Moreover, if you want to align against the mouse, why do
> an expensive (slow) BLAST against the entire nt database
> (most of which is non-mouse sequences).
> 
> If you are happy to run BLAST locally, setup a BLAST
> database of the mouse genome only, and BLAST against that.
> 
> Peter


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