[Bioperl-l] Context-sensitive alignment parameters
jason.stajich at duke.edu
Wed Jan 18 13:05:49 EST 2006
WABA kind of does this with three different match states.
On Jan 17, 2006, at 10:09 AM, Jay Moore wrote:
> Not strictly bioperl, but if anyone has any ideas, I would
> appreciate the feedback.
> I am doing some comparative work between partially-sequenced plant
> genomic DNA, and fully-sequenced Arabidopsis genome.
> When I am aligning sequences from other plants to Arabidopsis, the
> introns are much less well-conserved than the exons, and this ought
> to be the case
> for animals and other organisms too. Does anyone use make any
> allowance for this, by setting gap and gap-extension, or
> substitution matrix parameters
> in a context-sensitive way? Is there an alignment method that can
> take this kind of thing into account? Is it worth trying to take
> it into account
> Just wondered if anyone has a take, or any information, on this.
> Jay Moore
> Warwick HRI http://www.warwickhri.ac.uk
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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