[Bioperl-l] Re: perl code

[Ewan Birney]

On Sun, 21 Oct 2001, Holmes, Anna M. wrote:

> I am currently taking a bioinformativcs class in which we are supposed to
> find a perl module that converts dna/rna to aa sequence and aa sequence to a
> possible dna/rna code.  I am not able to access the Bio::Tools::CodonTable
> function.  Is it functional?  Is there another module that can be used?
> With what utilities?

It is functional.

You'll find that

  $seq = Bio::Seq->new( -seq => 'ATTGGTGAAATGTTTGG', -id => 'myid');

  $translated_seq = $seq->translate();

  # $translated_seq is a Bio::Seq object

  print "Translation is ",$translate_seq->seq,"\n"


works. Check out SeqIO system for reading and writing sequences as well.
Bio::Tools::CodonTable works fine, but most people don't need to access it
directly.

I've cc'd in the main bioperl list as people might be able to help there
and generally are more responsive than I am.



> 
> Assistance would be appreciated.
> 
> Sincerely,
> 
> Anna Holmes
>  
>