Difference between revisions of "Blast"

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m (Text replace - "Usage policy" to "Usage Policy")
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__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
 
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
 
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
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<!-- ########  Template Configuration ######## -->
 
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<!--Edit definitions of the variables used in template calls
 
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Required variables:
 
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app - lowercase name of the application e.g. "amber"
 
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url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
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Optional variables:
 
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INTEL - Version of the Intel Compiler e.g. "11.1"
 
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MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
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-->
 
 
{|
 
{|
 
<!--Main settings - REQUIRED-->
 
<!--Main settings - REQUIRED-->
 
|{{#vardefine:app|blast}}
 
|{{#vardefine:app|blast}}
 
|{{#vardefine:url|http://www.ncbi.nlm.nih.gov/books/NBK1763/}}
 
|{{#vardefine:url|http://www.ncbi.nlm.nih.gov/books/NBK1763/}}
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<!--Compiler and MPI settings - OPTIONAL -->
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
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|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
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|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
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<!--Choose sections to enable - OPTIONAL-->
 
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
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|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
 
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
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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 [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.
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<!--Location-->
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<!--Modules-->
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==Available Versions==
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==Required Modules==
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* 2.2.24.
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[[Modules|modules documentation]]
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* 2.2.25.
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===Serial===
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* 2.2.26 (default) - the current version of NCBI BLAST. Available on both EL5 and EL6 nodes.
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*ncbi_{{#var:app}}
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==System Variables==
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'''Note:''' we provide both NCBI BLAST+ and legacy blast binaries through the same modules.
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* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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<!-- -->
 
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{{#if: {{#var: mod}}|==Execution Environment and Modules==
 
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To use {{#var:app}} with the environment modules system at HPC the following commands are available:
 
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Get module information for {{lc: {{PAGENAME}}}}:
 
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$module spider ncbi_{{#var:app}}
 
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{{#if: {{#var:intel}}|Load Intel compiler: {{#tag:pre|$module load intel/{{#var:intel}}}}|}}{{#if: {{#var:mpi}}|Load MPI implementation: {{#tag:pre|$module load {{#var:mpi}}}}|}}
 
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Load the application module:
 
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$module load ncbi_{{#var:app}}
 
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To use a specific version, for example 2.2.24, run
 
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module load ncbi_blast/2.2.24
 
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The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
 
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* HPC_{{uc:{{#var:app}}}}_DIR - directory where {{#var:app}} is located.
 
 
* BLASTDB - location of the blast databases.
 
* BLASTDB - location of the blast databases.
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<!--Additional-->
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{{#if: {{#var: exe}}|==Additional Information==
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We provide both NCBI BLAST+ and legacy blast binaries through the same modules.
 
|}}
 
|}}
 
==BLAST databases==
 
==BLAST databases==
 
Follow the link to see the Information on the [[BLASTDB|UF HPC provided BLAST databases]].
 
Follow the link to see the Information on the [[BLASTDB|UF HPC provided BLAST databases]].
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{{#if: {{#var: exe}}|==Manual execution instructions==
 
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WRITE INSTRUCTIONS ON RUNNING THE APP WITHOUT MODULES HERE|}}
 
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}

Revision as of 17:44, 10 August 2012

Description

blast 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.

Required Modules

modules documentation

Serial

  • ncbi_blast

System Variables

  • HPC_{{#uppercase:blast}}_DIR - installation directory
  • BLASTDB - location of the blast databases.

Additional Information

We provide both NCBI BLAST+ and legacy blast binaries through the same modules.

BLAST databases

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




Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Blast&oldid=8338"