[Bioperl-l] Fetching particular tags of genbank/genpept features via eutils

Jason Stajich jason.stajich at gmail.com
Wed Sep 25 20:15:55 UTC 2013

More likely you want another place to ask the question - biostars perhaps - http://www.biostars.org/

if you were only searching genomes you could perhaps grab the ptt files from the FTP site - though you would need to lookup GI ids to get the ACC number for the NP_XX which is a bit convoluded and I'm not sure you can round trip.

But the produce descriptions for the genomes like in bacteria are in these .ptt files.


On Sep 24, 2013, at 11:00 PM, Alexey Morozov <alexeymorozov1991 at gmail.com> wrote:

> Dear colleagues,
> I'm not sure if this list is the right place to ask, but I have a question
> regarding NCBI eutils. Say, I have lots of CDS's IDs like NP_769305.1 or
> YP_001638012.1. "Lots" as in "Millions of them" (a metagenomic project). Of
> course, I want to get something actually meaningful, so I decided to use
> "product" field of associated protein records. Can I spare fetching
> complete records, which will easily be gygabytes upon gigabytes of
> unnecessary data and get at least only "protein" feature of genpept file?
> -- 
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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