Difference between revisions of "Blast"
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{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | ||
| − | See [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide Blast Program Selection Guide] and the main blast website for more details. | + | 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 [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide Blast Program Selection Guide] and the main blast website for more details. |
<!--Location--> | <!--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. | |
| + | * 2.2.25 (default) - the current version of NCBI BLAST. | ||
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{{#if: {{#var: mod}}|==Running the application using modules== | {{#if: {{#var: mod}}|==Running the application using modules== | ||
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HPC_{{uc:{{#var:app}}}}_DIR - directory where {{#var:app}} is located. | HPC_{{uc:{{#var:app}}}}_DIR - directory where {{#var:app}} is located. | ||
|}} | |}} | ||
| + | ==BLAST databases== | ||
| + | Follow the link to see the Information on the [[BLASTDB|UF HPC provided BLAST databases]]. | ||
{{#if: {{#var: exe}}|==Manual execution instructions== | {{#if: {{#var: exe}}|==Manual execution instructions== | ||
WRITE INSTRUCTIONS ON RUNNING THE APP WITHOUT MODULES HERE|}} | WRITE INSTRUCTIONS ON RUNNING THE APP WITHOUT MODULES HERE|}} | ||
Revision as of 18:54, 20 February 2012
Description
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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 - 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.
- 2.2.25 (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 blast_ncbi
Load the application module:
$module load blast_ncbi
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.
BLAST databases
Follow the link to see the Information on the UF HPC provided BLAST databases.