<p>Hi Peter,<br>
Thanks a lot, good to know there is remapper, but not in this case. Have to write my own.<br>
Jim </p>
<div class="gmail_quote">On Aug 19, 2014 5:35 AM, "Peter Cock" <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Jim,<br>
<br>
A small mock example might help to explain exactly what you<br>
want to do, but I would probably loop of the two aligned sequences<br>
looking for gaps and thus calculating the mapping (which I would<br>
probably store as a dictionary).<br>
<br>
See also <a href="http://biopython.org/wiki/Coordinate_mapping" target="_blank">http://biopython.org/wiki/Coordinate_mapping</a> - designed<br>
for something slightly different but perhaps relevant?<br>
<br>
Peter<br>
<br>
<br>
On Tue, Aug 19, 2014 at 1:13 AM, Jim Mailman <<a href="mailto:jimmailman1@gmail.com">jimmailman1@gmail.com</a>> wrote:<br>
> Hello everyone,<br>
> I have two sequences A and B with about 90% identity and a few small indels.<br>
> They are about 30kb long. If I align sequences A to B using either BLAST or<br>
> MUSCLE, for every base in A, how can I get the base coordinates of A aligned<br>
> to any given coordinates in B?<br>
> Is there something in Biopython to do this? Are there any existing tools for<br>
> this? I looked at the<br>
> Package Bio :: Package Blast :: Module Record :: Class HSP<br>
><br>
> If there is no existing tools, is this the best place to get started?<br>
><br>
> Thanks,<br>
><br>
> Jim<br>
><br>
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</blockquote></div>