[Bioperl-l] dna seq for an AA entry

[Ewan Birney]

On Sat, 26 May 2001, Hilmar Lapp wrote:

> "Saurabh D. Patel" wrote:
> > 
> > Now that my bioperl setup is working, I have another (newbie) question:
> > given a genbank accession number/amino acid sequence, is there any easy
> > way to get corresponding dna sequence?  I can think of a kludge where I
> 
> If there is a crosslink somewhere in the feature table (which I
> think there is in Genbank, but I'm not sure particularly where off
> the top of my head, and swissprot also has crosslinks), pull out
> that piece of annotation (e.g. scan the attached features) and
> retrieve the sequence entry using Bio::DB::GenBank or
> Bio::DB::EMBL (or Bio::DB::Universal :-))

I find this easier to do in the EMBL entries because the DR lines are more
explicit - they are in the $seq->annotation->each_DBLink() inside bioperl.

In genbank you will need to parse the seqfeatures and find the db_xref
tag.



> 
> 	Hilmar
> 
> -- 
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> Hilmar Lapp                              email: hilmarl@yahoo.com
> GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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