<p>Hi,</p>

<p>I'm interested in getting the scientific names of my blast hits ran locally. I see blast+ search apps have option <code>-outfmt</code> which can take <code>sscinames</code>(seems new in version Blast+ 2.2.28), but even using <code>nt</code> from NCBI(no luck with local databases either) I get <code>N\A</code> for this specifier. Similarity for '%S' of <code>-outfmt</code> in <code>blastdbcmd</code>.</p>

<p>For example:</p>

<pre><code>$ 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
</code></pre>

<p>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 <code>blastdbcmd</code> 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 <code>staxids</code>, so I can now get the taxid directly from the blast output.</p>

<p>So my questions is.</p>

<ul>
<li>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?</li>
</ul>

<p>In a side note. If there is a way, it seems odd NCBI's <code>nt</code> is not built using it. At least that is the case for the version I got from Jul 11 2013.</p>

<p>Thanks in advance,<br>
Carlos<br>
EDIT: I found I can now use <code>staxids</code> to simplify my life a little. Some additional question formatting. NT updated to version from Jul 11.</p>

<p>I indeed was able to find my answer in NCBI BLAST documentation:<br>
<a href='http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.Quick_start' title='BLAST Command Line Applications User Manual'>BLAST Command Line Applications User Manual</a></p>

<p>Basically the only taxonomy information stored directly in the BLAST database is the taxid. The rest needs to be pulled from an additional database also provided by NCBI:<br>
<a href='ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz'>ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz</a></p>

<p>As per the documentation make sure <code>taxdb</code> database is in the path defined by <code>BLASTDB</code> environment variable. After that you will be able to ask for several additional taxonomic information in the tabular output. For example:<br></p>

<pre><code>$ blastn -db nt -num_threads 24 -max_target_seqs 1 -outfmt '6 qseqid sseqid evalue bitscore sgi sacc staxids sscinames scomnames stitle' -query 229577210.fasta
gi|229577210|ref|NM_001743.4|   gi|229577210|ref|NM_001743.4|   0.0     2418    229577210       NM_001743       9606    Homo sapiens    human   Homo sapiens calmodulin 2 (phosphorylase kinase, delta) (CALM2), mRNA
</code></pre>
