[Bioperl-l] Graphical alignments with blast

[Jason Stajich]

On Tue, 16 Dec 2003, Mike Muratet wrote:

> Greetings
>
> I am trying to roll my own simple graphical alignment from blast data
> (unless of course someone already knows of one). As near as I can figure
> from bptutorial and the man pages, the approach would be create a set of
> LocatableSeq objects to manually create a SimpleAlign object. At that point,

You can already get this out with
 my $aln = $hsp->get_aln();

> one could write out a file which could be plotted with one of existing
> utilities, or use a Bio::Graphics object. Has anyone gone down this path?

As for drawing it - you want to see the alignment with the bases drawn
out, right?

Some of the glyphs in Bio::Graphics do allow for drawing pairwise
alignments pretty well, but I've only used them in the context of Gbrowse
- would be a useful example script to have working to show how to generate
this sort of thing from biographics.

Alternatively you can use something like alscript to generate the pretty
alignment:
 http://www.compbio.dundee.ac.uk/Software/Alscript/alscript.html

Boxshade may also provide what you want as well.

The pasteur site has a review of a bunch of software that falls in this
category here:
http://bioweb.pasteur.fr/cgi-bin/seqanal/review-edital.pl

>
> Thanks
>
> Mike
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu