Difference between revisions of "PLAST"
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|{{#vardefine:app|plast}} | |{{#vardefine:app|plast}} | ||
| − | |{{#vardefine:url| | + | |{{#vardefine:url|https://plast.inria.fr/}} |
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
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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] | ||
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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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{{#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: | ||
| − | + | 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 20:23, 12 August 2022
Description
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.
Environment Modules
Run module spider plast to find out what environment modules are available for this application.
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.