[Bioperl-l] Context-sensitive alignment parameters

[Jason Stajich]

WABA kind of does this with three different match states.

-jason
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
>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12