[Bioperl-l] Blast results question

Jason Stajich jason at cgt.duhs.duke.edu
Wed Feb 18 09:18:43 EST 2004

You might want to try using est2genome/sim4/spidey/exonerate on the
region where you have your multiple hits if you care about the splice
sites/predicting a gene structure.  use the start & end methods from a
Search::Hit object to get the min/max location of the hits in the hit
sequence $hit->start('hit'),$hit->end('hit'), extract this seq, and run
one of the EST->genome aligners.  Or are you just trying to locate this
approximate region of the genome in the first place?


On Wed, 18 Feb 2004, Sean Davis wrote:

> I have a large number of blast results against the (human) genome.  The
> query was a large number of oligos (from microarray) taken from various ESTs
> or full-length transcripts.  I have many that are "broken" by splice sites
> in the genome resulting in two different "hits" near each other.  Is there
> someone who has code or suggestions about how to "stitch" these hits back
> together?
> Thanks,
> Sean
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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