ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems

Motivation: BLAST remains one of the most widely used tools in computational biology. The rate at which new sequence data is available continues to grow exponentially, driving the emergence of new fields of biological research. At the same time, multicore systems and conventional clusters are more a...

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Autores principales: Oehmen, Christopher S., Baxter, Douglas J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597145/
https://www.ncbi.nlm.nih.gov/pubmed/23361326
http://dx.doi.org/10.1093/bioinformatics/btt013
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author Oehmen, Christopher S.
Baxter, Douglas J.
author_facet Oehmen, Christopher S.
Baxter, Douglas J.
author_sort Oehmen, Christopher S.
collection PubMed
description Motivation: BLAST remains one of the most widely used tools in computational biology. The rate at which new sequence data is available continues to grow exponentially, driving the emergence of new fields of biological research. At the same time, multicore systems and conventional clusters are more accessible. ScalaBLAST has been designed to run on conventional multiprocessor systems with an eye to extreme parallelism, enabling parallel BLAST calculations using >16 000 processing cores with a portable, robust, fault-resilient design that introduces little to no overhead with respect to serial BLAST. Availability: ScalaBLAST 2.0 source code can be freely downloaded from http://omics.pnl.gov/software/ScalaBLAST.php. Contact: christopher.oehmen@pnl.gov
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spelling pubmed-35971452013-03-14 ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems Oehmen, Christopher S. Baxter, Douglas J. Bioinformatics Applications Notes Motivation: BLAST remains one of the most widely used tools in computational biology. The rate at which new sequence data is available continues to grow exponentially, driving the emergence of new fields of biological research. At the same time, multicore systems and conventional clusters are more accessible. ScalaBLAST has been designed to run on conventional multiprocessor systems with an eye to extreme parallelism, enabling parallel BLAST calculations using >16 000 processing cores with a portable, robust, fault-resilient design that introduces little to no overhead with respect to serial BLAST. Availability: ScalaBLAST 2.0 source code can be freely downloaded from http://omics.pnl.gov/software/ScalaBLAST.php. Contact: christopher.oehmen@pnl.gov Oxford University Press 2013-03-15 2013-01-29 /pmc/articles/PMC3597145/ /pubmed/23361326 http://dx.doi.org/10.1093/bioinformatics/btt013 Text en © The Author 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Oehmen, Christopher S.
Baxter, Douglas J.
ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems
title ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems
title_full ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems
title_fullStr ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems
title_full_unstemmed ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems
title_short ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems
title_sort scalablast 2.0: rapid and robust blast calculations on multiprocessor systems
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597145/
https://www.ncbi.nlm.nih.gov/pubmed/23361326
http://dx.doi.org/10.1093/bioinformatics/btt013
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