[Biopython] convert coordinates from one sequence to another in an alignment

[Jim Mailman]

Hi Peter,
Thanks a lot, good to know there is remapper, but not in this case. Have to
write my own.
Jim
On Aug 19, 2014 5:35 AM, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:

> Hi Jim,
>
> A small mock example might help to explain exactly what you
> want to do, but I would probably loop of the two aligned sequences
> looking for gaps and thus calculating the mapping (which I would
> probably store as a dictionary).
>
> See also http://biopython.org/wiki/Coordinate_mapping - designed
> for something slightly different but perhaps relevant?
>
> Peter
>
>
> On Tue, Aug 19, 2014 at 1:13 AM, Jim Mailman <jimmailman1 at gmail.com>
> wrote:
> > Hello everyone,
> > I have two sequences A and B with about 90% identity and a few small
> indels.
> > They are about 30kb long. If I align sequences A to B using either BLAST
> or
> > MUSCLE, for every base in A, how can I get the base coordinates of A
> aligned
> > to any given coordinates in B?
> > Is there something in Biopython to do this? Are there any existing tools
> for
> > this? I looked at the
> > Package Bio :: Package Blast :: Module Record :: Class HSP
> >
> > If there is no existing tools, is this the best place to get started?
> >
> > Thanks,
> >
> > Jim
> >
> > _______________________________________________
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> > http://mailman.open-bio.org/mailman/listinfo/biopython
>
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