Difference between revisions of "PLAST"

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(Updated URL and Citations)
 
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{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|plast}}
 
|{{#vardefine:app|plast}}
|{{#vardefine:url|ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/}}
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|{{#vardefine:url|https://plast.inria.fr/}}
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
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|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:faq|}}            <!--FAQ-->
 
|{{#vardefine:faq|}}            <!--FAQ-->
|{{#vardefine:citation|}}      <!--CITATION-->
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|{{#vardefine:citation|1}}      <!--CITATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
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* Composition-based score adjustments as in Bioinformatics 21:902-911
 
* Composition-based score adjustments as in Bioinformatics 21:902-911
 
for plastp and tplastn.
 
for plastp and tplastn.
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 +
[https://github.com/PLAST-software/plast-library PLAST Source Code]
  
 
<!--Modules-->
 
<!--Modules-->
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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
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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If you publish research that uses {{#var:app}} you have to cite it as follows:
 
If you publish research that uses {{#var:app}} you have to cite it as follows:
  
WRITE_CITATION_HERE
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Nguyen VH, Lavenier D. (2009) PLAST: parallel local alignment search tool for database comparison. BMC Bioinformatics, vol 10, no 329.
  
 
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Latest revision as of 13:34, 21 February 2022

Description

plast website  

PLAST is a parallel alignment search tool for comparing large protein banks. PLAST runs 3 to 5 times faster than the NCBI-BLAST software when processing large amount of data.

The following features are currently available:

  • Protein vs protein (plastp), protein vs nucleotide (tplastn),

nucleotide vs protein (plastx) and nucleotide vs nucleotide (tplastx) searches.

  • Query filtering using SEG low complexity filters.
  • Karlin-Altschul alignment statistics.
  • Composition-based score adjustments as in Bioinformatics 21:902-911

for plastp and tplastn.

PLAST Source Code

Required Modules

Serial

  • plast

System Variables

  • HPC_PLAST_DIR - installation directory




Citation

If you publish research that uses plast you have to cite it as follows:

Nguyen VH, Lavenier D. (2009) PLAST: parallel local alignment search tool for database comparison. BMC Bioinformatics, vol 10, no 329.


Validation

  • Validated 4/5/2018