[Bioperl-l] taxonomy db flatfile: get taxon from gi?

Anna Friedlander anna.fr at gmail.com
Thu Nov 10 15:01:57 EST 2011


Hi all

Does anyone know if there is a way to get a Taxonomy node and/or
taxonid from a gi number using the flatfile with taxonomy db?

I have blast output that I want to append taxonomic information to. I
have hundreds of thousands of items to do this for, so it's not
practical to use entrez to query the NCBI database.

I have the GI->taxid file from the taxonomy ftp but it's 3.2GB so I
think much too large to put into a hash!

This was also discussed in 2009:
http://bioperl.org/pipermail/bioperl-l/2009-April/029751.html but I
don't think there was a conclusion?

Thanks for your help
Anna Friedlander



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