GPU-BSM: a GPU-based tool to map bisulfite-treated reads.

Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines r...

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Autores principales:	Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1b17c93489b54d569b57301154a1189b
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spelling	oai:doaj.org-article:1b17c93489b54d569b57301154a1189b2021-11-18T08:18:42ZGPU-BSM: a GPU-based tool to map bisulfite-treated reads.1932-620310.1371/journal.pone.0097277https://doaj.org/article/1b17c93489b54d569b57301154a1189b2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24842718/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads.Andrea ManconiAlessandro OrroEmanuele MancaGiuliano ArmanoLuciano MilanesiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 5, p e97277 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Andrea Manconi Alessandro Orro Emanuele Manca Giuliano Armano Luciano Milanesi GPU-BSM: a GPU-based tool to map bisulfite-treated reads.
description	Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads.
format	article
author	Andrea Manconi Alessandro Orro Emanuele Manca Giuliano Armano Luciano Milanesi
author_facet	Andrea Manconi Alessandro Orro Emanuele Manca Giuliano Armano Luciano Milanesi
author_sort	Andrea Manconi
title	GPU-BSM: a GPU-based tool to map bisulfite-treated reads.
title_short	GPU-BSM: a GPU-based tool to map bisulfite-treated reads.
title_full	GPU-BSM: a GPU-based tool to map bisulfite-treated reads.
title_fullStr	GPU-BSM: a GPU-based tool to map bisulfite-treated reads.
title_full_unstemmed	GPU-BSM: a GPU-based tool to map bisulfite-treated reads.
title_sort	gpu-bsm: a gpu-based tool to map bisulfite-treated reads.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/1b17c93489b54d569b57301154a1189b
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GPU-BSM: a GPU-based tool to map bisulfite-treated reads.

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