Ncbi Blast+ Taxid And Taxid_Map

Question

[Jelle]

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?

[Michael]

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

Answer 1

[Deniz Koellhofer]

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

[Jelle]

ah :(, well.. good to know.

[Michael]

Hi, any news about this?

Answer 2

[Joseph Hughes]

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