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

[Lincoln Stein]

The Boulder project is defunct in the sense that I'm no longer supporting it, 
but the source code is still available (and will always be available).  You 
can find it on CPAN, as well as at http://stein.cshl.org/software/boulder/.

The philosophy of Boulder is very different from Bioperl.  It's basically a 
hierarchical tag-value system in which each of the tags is an accessor 
method.  A small number of parsers were written to put biological file 
formats into Boulder format, but it is nothing compared to the huge number of 
parsers in Bioperl.

If someone wants to fold Boulder into Bioperl in some way, I will 
offer hints and advice.

Lincoln

On Friday 12 April 2002 13:23, Guoneng Zhong wrote:
> 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
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l@bioperl.org
> >> http://bioperl.org/mailman/listinfo/bioperl-l
> >
> > --
> > Jason Stajich
> > Duke University
> > jason@cgt.mc.duke.edu
>
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