[Biopython] API support for finding polymorphisms?

[Sean Davis]

On Mon, Oct 18, 2010 at 7:56 PM, Alex Lancaster <alexl at users.sourceforge.net
> wrote:

> Hi there,
>
> I have a number of already-aligned sequences from the same species and I
> can get them into Biopython as a multiple alignment using the following
>
> alignments=AlignIO.parse("foobar.fasta", "fasta")
>
> Before I go off and implement something by hand, I was wondering if
> there is any support for finding polymorphisms across the alignments,
> and, in particular, whether there is a way to "filter" the polymorphisms
> (as there are likely to be too many to look at manually) by type
> (e.g. stop codon gains/losses, frameshifts, or large deletions/
> insertions).
>
> I know that other packages such as samtools have ways to find
> polymorphisms with respect to a specified reference sequence (and I'm
> not sure, but I don't think samtools will allow you to filter by type in
> any case), but I'd like to find a biopythonish solution.
>
> I did a quick look through the API, Cookbook etc., but didn't find
> anything that quite matches what I'm trying to do.
>


Hi, Alex.  Are you working from short read data?  If so, what platform?  In
what format are the aligned data?

Sean