Difference between revisions of "Blast"

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==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.
 
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{{#if: {{#var: conf}}|==Configuration==
 
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{{#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]]
 
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{{#if: {{#var: faq}}|==FAQ==
 
{{#if: {{#var: faq}}|==FAQ==

Latest revision as of 21:01, 6 December 2019

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_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