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[Molecular-evolution] redundancy in BLAST

TO via mol-evol%40net.bio.net (by phidippus from yahoo.com)
Thu Sep 6 15:00:28 EST 2007


I am using BLAST to identify orthologs between two species A and B
where I know there are multiple transcripts for some genes in both
data sets. 

I read some papers where they said that redundancies were taken care
of using the longest sequence, etc. So this sounds like redundancies
were taken care of before running BLAST.

But it's also possible to take care of the redundancies after running
BLAST with data sets that contain the redundancies. 

Which way is more appropriate?

Thank you.

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