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