In ubuntu, the BLAST package is called blast2
sudo aptitude install blast2
This installs a whole bunch of blast commands for local and remote searching. For example, you can search NCBI with a list of fasta entries as queries (sequentially) using the remote NCBI server to do the work:
blastcl3 -p blastp -m 3 -v 10 -b 10 -i infile.fasta -o outfile.txt
Where, here I’m just looking for a few quick top hits. -p is the important option, where you define the search engine. In this example I’m using blastp to search protein. I think the default database is ncbi nr.
And here’s an example of searching a local database using your own cpu:
blast2 -p blastp -m 3 -v 10 -b 10 -i infile.fasta
and an outfile isn’t defined, so it just goes to standard out, ready for pipes.
