QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.

Multiple sequence alignment is a crucial task in a number of biological analyses like secondary structure prediction, domain searching, phylogeny, etc. MSAProbs is currently the most accurate alignment algorithm, but its effectiveness is obtained at the expense of computational time. In the paper we...

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Autores principales:	Adam Gudyś, Sebastian Deorowicz
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f6f8ad4afe0e4f0582ae8b3fba31270e
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spelling	oai:doaj.org-article:f6f8ad4afe0e4f0582ae8b3fba31270e2021-11-18T08:31:11ZQuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.1932-620310.1371/journal.pone.0088901https://doaj.org/article/f6f8ad4afe0e4f0582ae8b3fba31270e2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24586435/?tool=EBIhttps://doaj.org/toc/1932-6203Multiple sequence alignment is a crucial task in a number of biological analyses like secondary structure prediction, domain searching, phylogeny, etc. MSAProbs is currently the most accurate alignment algorithm, but its effectiveness is obtained at the expense of computational time. In the paper we present QuickProbs, the variant of MSAProbs customised for graphics processors. We selected the two most time consuming stages of MSAProbs to be redesigned for GPU execution: the posterior matrices calculation and the consistency transformation. Experiments on three popular benchmarks (BAliBASE, PREFAB, OXBench-X) on quad-core PC equipped with high-end graphics card show QuickProbs to be 5.7 to 9.7 times faster than original CPU-parallel MSAProbs. Additional tests performed on several protein families from Pfam database give overall speed-up of 6.7. Compared to other algorithms like MAFFT, MUSCLE, or ClustalW, QuickProbs proved to be much more accurate at similar speed. Additionally we introduce a tuned variant of QuickProbs which is significantly more accurate on sets of distantly related sequences than MSAProbs without exceeding its computation time. The GPU part of QuickProbs was implemented in OpenCL, thus the package is suitable for graphics processors produced by all major vendors.Adam GudyśSebastian DeorowiczPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 2, p e88901 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Adam Gudyś Sebastian Deorowicz QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.
description	Multiple sequence alignment is a crucial task in a number of biological analyses like secondary structure prediction, domain searching, phylogeny, etc. MSAProbs is currently the most accurate alignment algorithm, but its effectiveness is obtained at the expense of computational time. In the paper we present QuickProbs, the variant of MSAProbs customised for graphics processors. We selected the two most time consuming stages of MSAProbs to be redesigned for GPU execution: the posterior matrices calculation and the consistency transformation. Experiments on three popular benchmarks (BAliBASE, PREFAB, OXBench-X) on quad-core PC equipped with high-end graphics card show QuickProbs to be 5.7 to 9.7 times faster than original CPU-parallel MSAProbs. Additional tests performed on several protein families from Pfam database give overall speed-up of 6.7. Compared to other algorithms like MAFFT, MUSCLE, or ClustalW, QuickProbs proved to be much more accurate at similar speed. Additionally we introduce a tuned variant of QuickProbs which is significantly more accurate on sets of distantly related sequences than MSAProbs without exceeding its computation time. The GPU part of QuickProbs was implemented in OpenCL, thus the package is suitable for graphics processors produced by all major vendors.
format	article
author	Adam Gudyś Sebastian Deorowicz
author_facet	Adam Gudyś Sebastian Deorowicz
author_sort	Adam Gudyś
title	QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.
title_short	QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.
title_full	QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.
title_fullStr	QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.
title_full_unstemmed	QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.
title_sort	quickprobs--a fast multiple sequence alignment algorithm designed for graphics processors.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/f6f8ad4afe0e4f0582ae8b3fba31270e
work_keys_str_mv	AT adamgudys quickprobsafastmultiplesequencealignmentalgorithmdesignedforgraphicsprocessors AT sebastiandeorowicz quickprobsafastmultiplesequencealignmentalgorithmdesignedforgraphicsprocessors
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QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.

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