[Bioperl-l] (no subject)

Chris Fields cjfields at uiuc.edu
Mon Jul 21 12:42:37 EDT 2008


Ya beat me to it!  I agree, this is the best way to go, and it would  
save an extra BLAST run (though if you need it Diego's bl2seq  
suggestion is the way to go).

chris

On Jul 21, 2008, at 11:31 AM, Dave Messina wrote:

> You know which protein sequence corresponds to which cDNA sequence,  
> so I
> think you could also:
>
> - take the start and end coordinates of the domain in the protein  
> (from the
> HMMer output)
> - convert those into the start and end coordinates of the domain in  
> the cDNA
> - use the subseq() method to extract the subsequence of the cDNA
>
>
> Dave
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