[Molecular-evolution] redundancy in BLAST

[Georgiana May]

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  
define orthology.

Georgiana May
EEB
UMn



On Sep 6, 2007, at 3:00 PM, TO wrote:

> Hello,
>
> 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.
> Phidd.
>
>
>
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