[Bioperl-l] Fwd: Help

[Lincoln Stein]

I think this has been true for the past 8 months at least when I rewrote 
DB::Genbank to work through GI and accession numbers.  

Lincoln


On Friday 05 September 2003 02:57 pm, Aaron J. Mackey wrote:
> Begin forwarded message:
> > From: Preetam Shah <pshah at stanford.edu>
> > Date: Fri Sep 5, 2003  2:28:17 PM US/Eastern
> > To: amackey at virginia.edu
> > Subject: Help
> >
> >
> >
> > Dear Dr. Mackey,
> >      I was wondering if you could help me in any way. I saw you name
> > on the
> > web when I did a search on this matter. Currently NCBI's batch Entrez
> > allows me to download batch sequences with a file of Gi's and Accession
> > numbers. However I want to be able to download the only specific
> > sequences
> > based on GSS Ids eg. ENTIE01TF. I have done this in the past but NCBI
> > has
> > changed this...please see e-mail below. Do you have a script that might
> > help me extract this informaton. I can run Bioperl or perl but I am
> > not a
> > programmer. Any help is appreciated. I have to retrieve thousands of
> > sequences at a time and manually creating a file of Gi's or Accession
> > numbers is tedious. I have files of GSS Ids. Thanks for your help.
> >
> > E mail from NCBI:
> > Date:  Wed, 3 Sep 2003 18:10:45 -0400
> > From:  "Gabrielian, Andrei (NIH/NLM/NCBI)" <gabrieli at ncbi.nlm.nih.gov>
> > To:  'Preetam Shah' <pshah at stanford.edu>
> > Subject:  RE: Urgent
> > Dear NCBI user,
> > Batch Entrez that allowed to use anything except GB Id or gi, was
> > broken
> > (was doing all-fields search, whis is wrong). Now it is fixed, and it
> > accepts Genbank accession numbers or gi's only.
> > You can download the corresponding files from the FTP site and run the
> > script on them to fish out the necessary sequences. I do not see any
> > alternative.
> > Regards,
> > A.Gabrielian
> > NCBI Help desk
> >
> >
> > Regards,
> > Preetam Shah, Ph.D.
>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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