[Bioperl-l] Context-sensitive alignment parameters
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.
Warwick HRI http://www.warwickhri.ac.uk
More information about the Bioperl-l