[Bioperl-l] clarification on Bio::DB::GenBank

Osborne, Brian Brian.Osborne@osip.com
Thu, 5 Oct 2000 14:22:38 -0400

To the group,

First, congratulations to the developers on the exceptional work they
continue to do on bioperl. It's been my pleasure to watch the traffic as it
passes and see the graceful progress of this project. 

My question relates to get_Seq_by_id() from Bio::DB::GenBank (I'm using the
latest version, "pre3"). It looks like this works for nucleotide gi numbers
(4,5,7,9,1147, etc.) but not protein gi numbers (125109,124343,125074,
etc.). This doesn't surprise me given that entrez/query.fcgi can query
Nucleotide or Protein, apparently not both simultaneously
(query.fcgi?cmd=Search&db=Nucleotide&term="125074"&doptcmdl=GenPept works,
t. doesn't, for example). The same is true of the older entrez CGIs, I

Is there a plan to implement the retrieval of protein sequences using gi
numbers, say through the use of an additional argument, "protein" or
"nucleotide", or with additional methods or by catching the error and
requerying? Please bear in mind that "no" means I'll have to use my own
significantly-less-beautiful modules !

Thanks again,

Brian O.

Brian Osborne, Information Technology
OSI Pharmaceuticals
777 Old Saw Mill River Rd.
Tarrytown NY 10591
TEL 914 467 6291
FAX 914 345 3565