Hi,
I'm interested in getting the scientific names of my blast hits ran locally. I see blast+ search apps have option '-outfmt' which can take 'sscinames'(seems new in version Blast+ 2.2.28), but even using 'nt' from NCBI(no luck with local databases either) I get an empty field for this specifier. Similarity for '%S' of '-outfmt' in 'blastdbcmd', here I get 'N/A'.
For example:
$ blastdbcmd -db nt -entry 229577210 -outfmt '%a || %g || %T || %S || %t'
NM_001743.4 || 229577210 || 9606 || N/A || Homo sapiens calmodulin 2 (phosphorylase kinase, delta) (CALM2), mRNA
Until now I've been using taxids in a very convoluted way. I will get the GIs from my hits, then query the blast db using 'blastdbcmd' to get the taxid and then query the local copy of the NCBI taxonomy database with bioperl to get the scientific name. Now that I see blast+ seems to be able to directly output the scientific name, I would like to simplify things.
So my questions is.
- Is there a way to build local blast databases in a way so 'sscinames' can be used to output the scientific name in blast+ results?
In a side note. If there is a way, it seems odd NCBI's 'nt' is not built using it. At least that is the case for the version I got from May 4 2013.
Thanks in advance,
Carlos
