[Bioperl-l] Genbank parsing using Bioperl

[Sean Davis]

Prabu R wrote:
> Dear All,
> 
> I feel sorry for making a small mistake in my earlier mail
> 
> I am not actually using Genbank releases, But Refseq Genome build gbk 
> files of NCBI (ftp.ncbi.nih.gov/genomes/ <http://ftp.ncbi.nih.gov/genomes/>)
> 
> Those files are genbank formatted and contains Refseq IDs.
> 
> Kindly help.
> 
> R. Prabu
> 
> ----------------------------
> 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.

Just grab this file:

ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz

It contains the one-to-one mapping you are looking for in a 
tab-delimited format.

Sean