Difference between revisions of "Blast"
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To use {{#var:app}} with the environment modules system at HPC the following commands are available: | To use {{#var:app}} with the environment modules system at HPC the following commands are available: | ||
Revision as of 02:02, 10 August 2012
Description
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. See Blast Program Selection Guide and the main blast website for more details.
Available Versions
- 2.2.24.
- 2.2.25.
- 2.2.26 (default) - the current version of NCBI BLAST. Available on both EL5 and EL6 nodes.
Note: we provide both NCBI BLAST+ and legacy blast binaries through the same modules.
Execution Environment and Modules
To use blast with the environment modules system at HPC the following commands are available:
Get module information for blast:
$module spider ncbi_blast
Load the application module:
$module load ncbi_blast
To use a specific version, for example 2.2.24, run
module load ncbi_blast/2.2.24
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_BLAST_DIR - directory where blast is located.
- BLASTDB - location of the blast databases.
BLAST databases
Follow the link to see the Information on the UF HPC provided BLAST databases.