[Bioperl-l] Context-sensitive alignment parameters

Jay Moore jaymoore at plantkind.com
Tue Jan 17 10:09:44 EST 2006

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

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