[Bioperl-l] protal2dna and Bio::SimpleAlign

[Jason Stajich]

I'm not familiar with the script.

Bio::Align::Utilities does protein to DNA mapping for an alignment with 
the aa_to_dna_aln function.

-jason
On Jan 22, 2005, at 4:07 PM, Maureen L Coleman wrote:

> Hi.
> I'm trying to use the protal2dna script (downloaded from Pasteur site) 
> to convert protein alignments back to DNA alignments. It works in some 
> cases but not in others.  In the cases where it doesn't work, it pulls 
> out the same sequence twice instead of pulling out seq1 and seq2 from 
> my protein alignment.  Then when it tries to match it up with the 
> corresponding DNA sequence, it doesn't work - it matches prot1 with 
> dna1 (correctly) and prot1 with dna2 (incorrectly).
>
> I suspect this might be related to the name,start,end (nse) method in 
> Bio::SimpleAlign.  Any suggestions?
>
> Thanks,
> Maureen
>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/