[Bioperl-l] Context-sensitive alignment parameters
dnm_a at swbell.net
Wed Jan 18 12:57:40 EST 2006
> 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
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
Hope this helps,
WashU Genome Sequencing Center
dmessina at watson.wustl.edu
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