[Biopython] search ncbi automatically

[Lapointe, David]

Hi Jessica,

David Hibbett , at Clark Univ, had a program with a similar purpose. See http://www.clarku.edu/faculty/dhibbett/.

Genbank publishes daily updates which can be scanned for taxa with some biopython scripts. That would involve some downloading every day or so. Each file ranges from 10-100 Mb compressed,though some days there might be a 900 Mb file.  A new version of Genbank happens every 2 months so if you have  division ( VRL, PRI, etc) that interests you. you can download all of the pieces of that division and rsync when a new Genbank version comes around.

David
________________________________________
From: biopython-bounces at lists.open-bio.org [biopython-bounces at lists.open-bio.org] on behalf of Jessica Grant [jgrant at smith.edu]
Sent: Monday, April 09, 2012 4:29 PM
To: biopython at lists.open-bio.org
Subject: [Biopython] search ncbi automatically

Hello,

I am working on a phylogenomic pipeline and want to keep my database as up-to-date as possible.


I was wondering if there is a way to automatically search genbank on occasion (every month or so, or however often they release new data) to see if any new sequences have been added for the taxa we are working with.  Is there a way to run a script in the background that will just go out and do that for me, and let me know if it finds anything?

Thanks for your help!

Jessica



_______________________________________________
Biopython mailing list  -  Biopython at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython