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

[Guoneng Zhong]

Thanks.... I was told by Lincoln Stein that the Boulder project is by 
and large defunct.  So if I were to reimplement it, where can I get info 
on how it was done and more importantly what its interface was?  Is it 
still part of bioperl 1.0?  I don't see it on the docs...

G

On Friday, April 12, 2002, at 12:29 PM, Jason Stajich wrote:

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