BLAST¶

The Basic Local Alignment Search Tool can be used for sequence similarity searching. The bundle packages NCBI BLAST version 2.16.0.

Usage example¶

The following command can be executed in the terminal to load the bundle:

1	`module load blast`

The module makes the following commands available:

blastn
blastp
blastx
makeblastdb
psiblast
rpsblast
rpstblastn
tblastn
tblastx
blastdbcheck
blastdbcmd

The blast_shell command can be used to access a shell in the bundle.

Run pet list -t blast for a list of examples. Examples taken from tinybio

Performance notes¶

No performance notes available

Recommended resources per session¶

BLAST should be run on a system with at least 16 GB of RAM and 8 threads. The recommendation were taken from University of Manitoba.

Benchmarks¶

No benchmarks available.

Community guides and tutorials¶

No community guides available.

Official site and documentation¶

Licensing information¶

NCBI BLAST is licensed under the Public Domain.

Primary citation¶

Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. 2009. BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.

External guides and resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za