[Bioperl-l] Context-sensitive alignment parameters

[Jay Moore]

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