[Bioperl-l] protal2dna and Bio::SimpleAlign

[Catherine Letondal]

On Jan 23, 2005, at 3:19 PM, Jason Stajich wrote:

> I'm not familiar with the script.

Web:
http://bioweb.pasteur.fr/seqanal/interfaces/protal2dna.html
Man:
http://bioweb.pasteur.fr/docs/man/man/protal2dna.1.html
Ftp:
ftp://ftp.pasteur.fr/pub/GenSoft/unix/alignment/protal2dna

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

The problem with this function aa_to_dna_aln is that  is restricted to 
frame 1 and to the standard genetic code, right?
        aa_to_dna_aln

         Title   : aa_to_dna_aln
         Usage   : my $dnaaln = aa_to_dna_aln($aa_aln, \%seqs);
         Function: Will convert an AA alignment to DNA space given the
                   corresponding DNA sequences.  Note that this method 
expects
                   the DNA sequences to be in frame +1 (GFF frame 0) as 
it will
                   start to project into coordinates starting at the 
first base of
                   the DNA sequence, if this alignment represents a 
different
                   frame for the cDNA you will need to edit the DNA 
sequences
                   to remove the 1st or 2nd bases (and revcom if things 
should be).
         Returns : Bio::Align::AlignI object
         Args    : 2 arguments, the alignment and a hashref.
                   Alignment is a Bio::Align::AlignI of amino acid 
sequences.
                   The hash reference should have keys which are
                   the display_ids for the aa
                   sequences in the alignment and the values are a
                   Bio::PrimarySeqI object for the corresponding
                   spliced cDNA sequence.


The other problem when using tools offering several genetic code (these 
sequences need a bacterial genetic code), is that the start codon of 
this code is not the right one. These sequences need: GTG=M (and not 
V).

>
> -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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l