[Biopython] align sequence to genomic DNA

[Peter Cock]

Hi Horea,

On Sat, Feb 28, 2015 at 5:47 AM, Horea Chrristian <h.chr at mail.ru> wrote:
> 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....

If you don't want to install any local software, databases or
copy of the mouse genome, then NCBI BLAST is probably
quite a good solution (especially given the low volume of
data - just two queries).

> 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

BLAST alignments include the start/end coordinates of the match
on both the query sequence and the match/hit sequence.

Peter