[Bioperl-l] Fwd: Help

[Aaron J. Mackey]

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.
>
>
>
>
>