Difference between revisions of "PLAST"
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Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
Johnbullard (talk | contribs) (Updated URL and Citations) |
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{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#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)--> | ||
|{{#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--> | + | |{{#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. | ||
| + | |||
| + | [https://github.com/PLAST-software/plast-library PLAST Source Code] | ||
<!--Modules--> | <!--Modules--> | ||
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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. | |
|}} | |}} | ||
Revision as of 13:34, 21 February 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.
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