[Bioperl-l] Question

[Jason Stajich]

On Tue, 17 Sep 2002, Perl yang wrote:

> I am trying to write one. Can I use perl to achieve
> it? Or do I have to use the NCBI toolkit? Does anyone
> have any suggestions about which functions in the NCBI
> toolkit that I should use? Or can anybody build a new
> fuction for that? That will be greatly helpful.
>

No need to touch the NCBI toolkit - you just need to do this via CGI
scripts with HTTP get and post - you would just need to extend the current
system we have in place - you can start with the example scripts that NCBI
provides as part of their eutils and see if they can be extended and then
wrapped into the existing Bio::DB::GenBank object.

-jason

> Thank you very much.
>
> Peter Yang
>
>
> --- Jason Stajich <jason@cgt.mc.duke.edu> wrote:
> > It can't be done right now.
> >
> > Eventually when someone wants to write the hook into
> > Entrez query system
> > this will be possible - will need a new function for
> > this.  Should be
> > quite simple but it requires a 2-query system where
> > you send the Entrez
> > query and get a list of GIs and then a subsequence
> > query to get the
> > sequence information.  Our current retrieval model
> > assumes sequence
> > identifiers as queries and gets back a set of
> > sequences.
> >
> > -jason
> >
> > On Mon, 16 Sep 2002, Perl yang wrote:
> >
> > > Hi,
> > >
> > > I want to use Bio::DB::GenBank to retrieve
> > Sequence by
> > > name, eg. "ribonucleoside reductase". There are
> > only
> > >
> > > $get_Seq_by_id, get_Seq_by_acc,
> > get_Seq_by_version,
> > > and get_Seq_by_gi('405830').
> > >
> > > How can I retrieve it by name. I don't want to use
> > the
> > > www way.
> > >
> > > Any suggestions? Thank you.
> > >
> > >
> > >
> > > __________________________________________________
> > > Do you Yahoo!?
> > > Yahoo! News - Today's headlines
> > > http://news.yahoo.com
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
> >
>
>
> __________________________________________________
> Do you Yahoo!?
> Yahoo! News - Today's headlines
> http://news.yahoo.com
>

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