[Bioperl-l] Get variation included in genbank file

[Dave Messina]

Hi Jessica,

Please keep the BioPerl list on the Cc line so everyone can follow along.


> Follow your approach it did not seem to me you can have Variation tag included which
> list the know dbSNP location, id and allele changes?

Ah okay, I assumed the file you attached was obtained directly from Genbank and that the variation info therein was already included. (It appears that's not the case — the variation information is not present in the version of NG_011506 I found at Genbank.)

If you want to include your own custom information in a genbank file, you'll have to pull it out of dbSNP (or wherever the variation info is). There are a couple of scripts that might be able to help with that (search for snp):

	http://www.bioperl.org/wiki/Bioperl_scripts


You can then insert them into a RichSeq object as features and output in genbank format. For that part, see the HOWTO:

	http://www.bioperl.org/wiki/HOWTO:Feature-Annotation


Dave