[Bioperl-l] Genbank parsing using Bioperl

Sean Davis sdavis2 at mail.nih.gov
Fri Apr 21 09:21:20 EDT 2006

On 4/21/06 6:45 AM, "Prabu R" <prabubio at gmail.com> wrote:

> Dear all!
> I am a novice bioperl user, trying to parse Genbank files with Bioperl
> modules to get some specific features and details.
> Anyone please tell me, whether we can retrive a Gene, its Transcript ID and
> its Protein ID from the Genbank file.
> I mainly need to extract with one to one relationship between TranscriptID
> and Protein ID.
> I was trying this. I was able to take these details if the gene is not
> alternatively spliced.
> If a gene contains multiple mRNA/CDS feature, I am not able to build the
> relationship between Transcript and its Protein.
> Kindly help me to find out whether this is possible in Bioperl.

See here:


However, genbank is only a repository, so not every transcript is going to
necessarily have a protein annotation, I don't think.  You might want to
look into using something like the RefSeq set (from NCBI) or Ensembl, both
of which have very rich annotation associated with their


More information about the Bioperl-l mailing list