How to add additional common names to a blast database

Question

[ranlib]

blastn with nt as a database can also return scientific name and common name of the blast hit via sscinames and scomnames in outfmt.

I can get that also if I make my own blast database if I add -taxid_map gi_taxid_nucl.dmp in makeblastdb

But how do I add a common name to a scientific name if the common name is missing, or better yet how do I add additional common names for a scientific name so I get output like the following in my blast matches:

momordica charantia     mellow fruit; bitter squash; karellabitter; bitter melon; bitter gourd; melon

Thanks so much in advance.

[Chris S.]

I would contact NCBI and find out how to create your own taxdb.btd and .bti files - I could not find any scripts to do so. Or maybe hack the preformatted taxdb.btd and add missing or extra common names?

[Istvan Albert]

yes, the whole taxonomy framework seems to be quite under documented.

Answer 1

[ryan.m.harrison]

First: Step-by-step guide to building your taxdb, including a simple (but hack) way of generating your taxid_map.txt file (gi or accession, and NCBI species ID): http://www.verdantforce.com/2014/12/building-blast-databases-with-taxonomy.html

Second: You'll want to use blastn output specifies, e.g. "staxids" "sscinames" "scomnames" "sblastnames" etc., to grab the appropriate name.