Blast

BLAST can be loaded using the following command;

 [user@ernie ]# module load BLAST/blast-2.2.26

This loads both blast-2.2.26 and ncbi-blast-2.2.26+, giving you access to commands such as;

 blastall blastclust blastdb_aliastool blastdbcheck blastdbcmd blast_formatter blastn blastp blastpgp blastx             

There are several ncbi databases installed on the HPC;

 16SMicrobial env_nt nt refseq_protein refseq_rna nr 

These are automatically checked every two weeks and updated if the blast update script finds newer versions.

The database directory is located;

 /ibers/ernie/scratch/databases/blast

For more databases to be added, simply email the HPC Systems Administrator.

An example blast

 blastall -p blastn -d /ibers/ernie/scratch/databases/blast/nt -i myfile.fasta -o myfile.blast -m 8

For some advice about running BLAST, take a look at [[Running BLAST optimally]]