[Bioperl-l] protal2dna and Bio::SimpleAlign

[Marc Logghe]

Guess, this is the bioperl implementation of EMBOSS tranalign ?
http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Apps/tranalign.html

ML

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of 
> Jason Stajich
> Sent: Monday, January 24, 2005 4:42 PM
> To: Catherine Letondal
> Cc: bioperl-l at portal.open-bio.org; Maureen L Coleman
> Subject: Re: [Bioperl-l] protal2dna and Bio::SimpleAlign
> 
> 
> 
> On Jan 24, 2005, at 10:28 AM, Catherine Letondal wrote:
> 
> >
> > 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
> >
> This is an alignment mapper routine not an alignment routine 
> itsself.  
> So I think I was just being stupid and not looking at what protal2dna 
> really was doing.
> 
> You provide it the protein multiple sequence alignment alignment and 
> the coding sequence which gave rise to it.  It maps the gaps 
> back in so 
> you have a CDS alignment.  Very basic iterating through the alignment.
> 
> So it has to all be in-frame and already spliced, it should have been 
> called aa_to_cds_aln.
> 
> The method is intended for getting ready to do Ka/Ks type 
> stuff so that 
> you have aligned  the sequences on codon boundaries and with 
> knowledge 
> about conservative aa replacements.
> 
> apologies for inciting confusion...
> -j
> 
> >         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
> >
> >
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
> 
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