[Bioperl-l] ORF FInder

[Heikki Lehvaslaiho]

Lynn,

Closest you get is translate_6frames() which can be called like:

  @seqs = Bio::SeqUtils->translate_6frames($nucseq);

You are more than welcome to eleborate on that (using methods
is_start_codon() and is_ter_codon() in Bio::Tools::CodonTable) to determine
ORFs to return. 

I think:

  @cdss = Bio::SeqUtils->orfs($nucseq, $min_orf_len);

would be useful. I'd love to include that into Bio::SeqUtils.


	-Heikki


Lynn Stevens wrote:
> 
> Is there a module in BioPerl which allows you to take a sequence and get
> back a list of all the ORFs (or even just the largest ORF) in all six frames
> (or even just one frame) indexed by sequence position.
> 
> In other words you would submit a seq object and you would get back a set of
> numbers which tell you where the ORFs are located in the sequence.
> 
> I have looked through all the documentation and still can not find this
> feature even though it seem like an extremely common task.
> 
> Thanks for any help,
> 
> Lynn
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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