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

[Jim Mailman]

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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