[Bioperl-l] no way to get protein/cDNA from species name?

[Jason Stajich]

Nope.
You can
a) go to the model organism site if it is a model organism
b) go to NCBI - select protein
Enter into the query box:
 Caenorhabditis briggsae[Organism]
hit go.
Select FASTA from menu, Hit text button.
Save to file.  Now you have a db of all C.briggsae proteins in genbank.

c) use Boulder::GenBank which allows you to specify a species name


Maybe consider helping out bioperl by seeing how we might be able to use
the Entrez query within bioperl either by migrating from Boulder or
reimplementing it.


On Fri, 12 Apr 2002, Guoneng Zhong wrote:

> Hi,
> So is there no way to get a list of protein proteins or even cDNA
> sequences based on a species name?  I am looking for hypothetical
> proteins.
>
> Thanks,
> G
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu