Question: Ncbi Blast+ Taxid And Taxid_Map
4
gravatar for Jelle
8.6 years ago by
Jelle50
Netherlands
Jelle50 wrote:

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?

ADD COMMENTlink modified 3.7 years ago by Joseph Hughes2.7k • written 8.6 years ago by Jelle50

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

ADD REPLYlink written 7.4 years ago by Michael Dondrup46k
9
gravatar for Deniz Koellhofer
8.6 years ago by
Deniz Koellhofer90 wrote:

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

ADD COMMENTlink written 8.6 years ago by Deniz Koellhofer90
1

ah :(, well.. good to know.

ADD REPLYlink written 8.6 years ago by Jelle50

Hi, any news about this?

ADD REPLYlink written 7.4 years ago by Michael Dondrup46k
0
gravatar for Joseph Hughes
3.7 years ago by
Joseph Hughes2.7k
Scotland, UK
Joseph Hughes2.7k wrote:

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

ADD COMMENTlink written 3.7 years ago by Joseph Hughes2.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1168 users visited in the last hour