[Bioperl-l] taxonomy ID
Russell.Smithies at agresearch.co.nz
Tue Mar 31 16:06:35 EDT 2009
The taxonomy information isn't in the blast output unless you created custom fasta headers for your blast database.
The easiest way to get the tax_id for your accessions would be to download the gi->tax_id list from ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz.
If you load that file into a hash, parse the accessions out of the blast hits then lookup the tax_id from that hash, I think it should be fairly fast.
Checking which are prokaryotes and which are eukaryotes based on tax_id is a separate problem :-)
If you grab the taxdump.tar.gz file from the same site, the nodes.dmp file contained within lists what division each tax_id belongs to (Bacteria, Invertebrates, Mammals, Phages, Plants, etc) so you can probably work it out from that.
It's not a very BioPerly solution but sometimes just looking up the answer from a file/table/hash is the simplest way.
Hope this helps,
Bioinformatics Applications Developer
T +64 3 489 9085
E russell.smithies at agresearch.co.nz
Invermay Research Centre
T +64 3 489 3809
F +64 3 489 9174
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of shalabh sharma
> Sent: Wednesday, 1 April 2009 7:43 a.m.
> To: bioperl-l
> Subject: [Bioperl-l] taxonomy ID
> Hi All,
> I am writing a script, for one of its part i have to parse a blast
> report (refseq blast) and check how may organisms are eukaryotes and how
> namy of them are prokaryotes.
> I am using BIO::DB::taxinomy module:
> But for this i need a taxonomyid (like '33090') given in the example.
> So is it possible to get a taxonomyid from refseq balst report?
> If not then how i can deal with this problem?
> i would really appreciate if anyone can help me out.
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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