[Bioperl-l] protal2dna and Bio::SimpleAlign

[Maureen L Coleman]

Thanks for the responses.  The problem (with both protal2dna and 
tranalign), as Catherine recognized, is that even when I specify 
Bacterial translation, it doesn't recognize my alternative start codons 
(gtg,ctg,ttg can all be Met).

As the quickest route, I went through and changed all my alternative 
start codons in the alignments to their "normal" translation.  Then 
protal2dna and tranalign seem to work fine.  aa_to_dna_aln should work 
for me too, since I already have the coding DNA sequences pulled out.

thanks again,
maureen

On Monday, January 24, 2005, at 10:41  AM, Jason Stajich wrote:

>
> 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
>>>>
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>>>>
>>>>
>>> --
>>> Jason Stajich
>>> jason.stajich at duke.edu
>>> http://www.duke.edu/~jes12/
>>>
>>> _______________________________________________
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>>
>>
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>