[Bioperl-l] producing an organism report from BLAST results?

Jason Stajich jason.stajich at duke.edu
Mon Nov 21 16:00:32 EST 2005

You need to look up the taxonomid ID from the gi number for a record.

So you do:
gi -> taxid
taxid -> species string

You can download the two column datafile from NCBI for all the GIs  
(separated by protein and nt) from


On Nov 21, 2005, at 1:49 PM, Tim Reid wrote:

> i am trying to reproduce the NCBI's html organism report of BLAST  
> results,
> but i can't figure out how they obtain taxonomy information for  
> each hit.
> as far as i can tell this information is not contained within a hit  
> object,
> although it is sometimes embedded in the description string.
> i have looked at the Bio::Taxonomy::FactoryI interface, which would  
> appear
> to offer some sort of solution by way of passing the entire  
> description
> string to the fuzzy_search method, but i cannot seem to find an
> implementation for this interface.
> also, Bio::DB::Taxonomy::entrez seemed promising except that it  
> does not
> appear to return any results when passed a description string.
> i would appreciate some help. how does the NCBI's organism report  
> generator
> work?
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Jason Stajich
Duke University

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