I don't see any problem with doing both, using longest sequences and
running BLAST. I see a problem in identifying orthologs in this way,
without any further analysis. Sequence similarity alone does not
On Sep 6, 2007, at 3:00 PM, TO wrote:
>> 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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