[Bioperl-l] Context-sensitive alignment parameters

Jason Stajich 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
> anyway?
> 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
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
Duke University

More information about the Bioperl-l mailing list