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Ncbi Blast+ Taxid And Taxid_Map

2 related questions. How does the -taxid argument for the NCBI's blast-2.2.24+ makeblastdb command work? When I execute:

makeblastdb -title "BO" -dbtype nucl -out BO -in BO.fna -parse_seqids -taxid 3712 -logfile testing.log
I assume all identifiers are linked to taxon id 3712. However when retrieving a particular sequence with:
blastdbcmd -db BO -entry B_oleracea-2 -outfmt "%T"
it results in a plain "0" Same for the taxid_map, first what is the correct formatting for the taxid_map? From the manual I can only find this:
4.6.8.10 taxid_map: Name of file which provides a mapping of sequence IDs to taxonomy IDs.
For me this suggest something like (whitespace either being a space or a tab)
B_oleracea-1 3712
B_oleracea-2 3712

However I cannot make this work - also results in a "0" when retrieving a single identifier with -outfmt "%T".

Any ideas?

blast ncbi makeblastdb taxonomy fasta

Hi, I would need this feature now, do you whether or not it is working in latest release?

2 answers

I've contacted the NCBI-BLAST support team and got a reply that the taxid_map isn't functional in this version. They are working on a bug fix for the upcoming releases. Cheers, Deniz

ah :(, well.. good to know.

It works now, for details on installation read this: http://www.ncbi.nlm.nih.gov/books/NBK279680/

Also the following Booster question and answer is useful: Scientific Names In Blast Output And Databases

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