Difference between revisions of "Blast"

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__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
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[[Category:Software]][[Category:Biology]][[Category:Genomics]]
 
{|
 
{|
 
<!--Main settings - REQUIRED-->
 
<!--Main settings - REQUIRED-->
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|1}} <!--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-->
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|{{#vardefine:job|1}} <!--Enable PBS script wiki page link-->
 
|{{#vardefine:policy|}} <!--Enable policy section -->
 
|{{#vardefine:policy|}} <!--Enable policy section -->
 
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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.
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
[[Modules|modules documentation]]
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
*ncbi_{{#var:app}}
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* BLASTDB - location of the blast databases.
 
* BLASTDB - location of the blast databases.
 
<!--Additional-->
 
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{{#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.|}}
{{#if: {{#var: pbs}}|==PBS Script Examples==
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{{#if: {{#var: job}}|==Job Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
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See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.|}}
 
{{#if: {{#var: policy}}|==Usage Policy==
 
{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
Performance comparison for the NCBI distributed binary 'blastn' vs binaries built by us from source using Intel's 2013 compiler or Open64 compiler.
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Performance comparison for the NCBI distributed binary 'blastn' vs binaries built by us from source using Intel's 2013 compiler or Open64 compiler. The open64 build behaves as a single-threaded build. The test data is a set of 2011229 nucleotide sequences used for the database and its subset of 1000 sequences is used as a query file.
  
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[[file:2015-07-20-blastn-binary_intel_open64.png]]
 
|}}
 
|}}
 
{{#if: {{#var: faq}}|==FAQ==
 
{{#if: {{#var: faq}}|==FAQ==

Latest revision as of 18:17, 12 August 2022

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.

Environment Modules

Run module spider blast to find out what environment modules are available for this application.

System Variables

  • HPC_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 UFRC provided BLAST databases.

Job Script Examples

See the Blast_Job_Scripts page for blast Job script examples.

Performance

Performance comparison for the NCBI distributed binary 'blastn' vs binaries built by us from source using Intel's 2013 compiler or Open64 compiler. The open64 build behaves as a single-threaded build. The test data is a set of 2011229 nucleotide sequences used for the database and its subset of 1000 sequences is used as a query file.

2015-07-20-blastn-binary intel open64.png