[Bioperl-l] Extraction of exon, intron, promoter, UTR

Jens Lichtenberg lichtenj at ohio.edu
Fri Mar 13 14:40:17 EDT 2009


Dave,

 

I am trying to extract in particular the exon/intron information stored in the Gene Table view of the Genbank entry at NCBI. It seems that that information does not get integrated into the information extracted for the SeqIO object retrieved from Genbank.

 

I would like to use the exons and intron from the feature object of the SeqIO but often the annotation in the Genbank entry is not as complete as the one in the Gene Table.

 

The Ensembl API provides good features for this support, however Ensembl is limited in the organisms that are currently supported.

 

Jens

 

From: dave at davemessina.com [mailto:dave at davemessina.com] On Behalf Of Dave Messina
Sent: Friday, March 13, 2009 1:48 PM
To: Jens Lichtenberg
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Extraction of exon, intron, promoter, UTR

 

Hey Jens,

 

>From what type of data are you trying to extract feature information?

 

BioPerl can extract features from many different types of data sources, such as Genbank, UniProt, Ensembl, NCBI.

 

See the feature HOWTO <http://www.bioperl.org/wiki/HOWTO:Feature-Annotation>  for some examples.

 

 

Dave

 




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