[Biopython] align sequence to genomic DNA

[Horea Chrristian]

Hi again Peter,

Thanks for the answer:

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

Is there any convenient way to access these values from within
biopython? Quite frankly I can't even find them by looking at the XML
https://bpaste.net/show/3c2d54393feb (the output is huge, this is just
the part that fit into my console).

So, can you show me how to get those values?

Best,
Christian



On Mon, 2015-03-02 at 13:24 +0000, Peter Cock wrote:

> 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


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