Difference between revisions of "Blast"
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The database directory is located; | The database directory is located; | ||
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For more databases to be added, simply email the HPC Systems Administrator. | For more databases to be added, simply email the HPC Systems Administrator. | ||
Revision as of 13:51, 21 October 2013
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 /cm/shared/apps/BLAST/ncbi-blast-2.2.26+/db/nt -i myfile.fasta -o myfile.blast -m 8
For some advice about running BLAST, take a look at [[Running BLAST optimally]]
