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
N\A for this specifier. Similarity for '%S' of
$ 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. I'm already able to simplify things a little using the also new output format specifier
staxids, so I can now get the taxid directly from the blast output.
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 Jul 11 2013.
Thanks in advance,
EDIT: I found I can now use
staxids to simplify my life a little. Some additional question formatting. NT updated to version from Jul 11.