[Biopython] align sequence to genomic DNA

[Peter Cock]

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