[Bioperl-l] retrieven ids

Dave Messina dmessina at wustl.edu
Wed Feb 28 14:31:29 EST 2007


Whenever I'm unsure of how to do something, I first look to see if one of
the  HOWTOs on bioperl.org covers it. In this case, the Features HOWTO has
example code which I think will do what you want.

Genbank records typically have the coding sequence of a protein as a
feature, so I would do something like:

- use the RefSeq protein IDs to query Entrez and get back the Genbank
records.

- read the Features HOWTO to refresh my memory on the syntax for grabbing
features.

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

- whip up a little script to loop through the Genbank records one at a
time with SeqIO and pull out the cDNA sequence features.


Dave




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