[Bioperl-l] Multiple alignments and Biographics

Jason Stajich jason at cgt.duhs.duke.edu
Tue May 4 12:59:13 EDT 2004

I do it by making the 'alignment' the reference.

This means grabbing the position of the start and end of each sequence in
the alignment - you bascially want to call for each sequence in the

$start = $seq->column_from_residue_number(1);
$end   = $seq->column_from_residue_number($seq->length);
and make new features out of these start/end positions.

You'll need to remap the oligo alignment position in the same way you
depending on how you have the coordinates stored (relative to the aligned
transcript sequences or just against a single trainscript).
Bio::Coordinate has some utils to help with this although the arithmetic
shouldn't be too hairy.


On Tue, 4 May 2004, Sean Davis wrote:

> Dear all,
> I am interested in forming multiple alignments between transcripts from the
> same gene cluster and rendering them using biographics.  I have alignments
> (from blast) from a set of oligos that I then want to include in the
> alignment.  Since multiple alignments do not have a "reference" sequence in
> this case, can anyone give me ideas about how to approach the problem with
> biographics?
> Thanks,
> Sean
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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