Difference between revisions of "Blast"

Revision as of 15:13, 29 March 2012

Description

{{{name}}} website
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.

Running the application using 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

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

To use a specific version, for example 2.2.24 run

module load ncbi_blast/2.2.24

HPC_BLAST_DIR - directory where blast is located.

BLAST databases

Follow the link to see the Information on the UF HPC provided BLAST databases.

@@ Line 35: / Line 35: @@
 <!--Location-->
 ==Available Versions==
-* 2.2.24 - the last NCBI BLAST version that featured the "megablast" and the "blastall" programs. If you are using an older pipeline that requires those programs please use the ncbi_blast/2.2.24 module.
+* 2.2.24.
-* 2.2.25 (default) - the current version of NCBI BLAST.
+* 2.2.25.
+* 2.2.26 (default) - the current version of NCBI BLAST.
 <!-- -->
 {{#if: {{#var: mod}}|==Running the application using modules==
@@ Line 49: / Line 50: @@
 The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
+To use a specific version, for example 2.2.24 run
+ module load ncbi_blast/2.2.24
 HPC_{{uc:{{#var:app}}}}_DIR - directory where {{#var:app}} is located.
 |}}