[Bioperl-l] Context-sensitive alignment parameters

David Messina dnm_a at swbell.net
Wed Jan 18 12:57:40 EST 2006

Hi Jay,

> 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?

I would do a local alignment  (with e.g. Blast) first to find the  
segments of the genome that match. Then, I would realign each of the  
matching segments using a global alignment algorithm (e.g. needle  
from the EMBOSS package) to force the best alignment within each  
matching region.

It's worth it if you're interested in looking at the overall  
conservation between the genomes or something like that.

If however you're just interested in the exons, then it's easier to  
do the alignments with cDNA representations of the sequences from the  
other plants and align those to the Arabidopsis genomic sequence  
(using Blast).

Hope this helps,

Dave Messina
Informatics Analyst
WashU Genome Sequencing Center
dmessina at watson.wustl.edu

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