{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T11:50:04Z","timestamp":1783079404134,"version":"3.54.6"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":480,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: DNA methylation analysis suffers from very long processing time, as the advent of Next-Generation Sequencers has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. As it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed.<\/jats:p>\n               <jats:p>Results: We present a new software tool, called HPG-Methyl, which efficiently maps bisulphite sequencing reads on DNA, analyzing DNA methylation. The strategy used by this software consists of leveraging the speed of the Burrows\u2013Wheeler Transform to map a large number of DNA fragments (reads) rapidly, as well as the accuracy of the Smith\u2013Waterman algorithm, which is exclusively employed to deal with the most ambiguous and shortest reads. Experimental results on platforms with Intel multicore processors show that HPG-Methyl significantly outperforms in both execution time and sensitivity state-of-the-art software such as Bismark, BS-Seeker or BSMAP, particularly for long bisulphite reads.<\/jats:p>\n               <jats:p>Availability and implementation: Software in the form of C libraries and functions, together with instructions to compile and execute this software. Available by sftp to anonymous@clariano.uv.es (password \u2018anonymous\u2019).<\/jats:p>\n               <jats:p>Contact: \u00a0juan.orduna@uv.es or jdopazo@cipf.es<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv357","type":"journal-article","created":{"date-parts":[[2015,6,12]],"date-time":"2015-06-12T02:49:45Z","timestamp":1434077385000},"page":"3130-3138","source":"Crossref","is-referenced-by-count":10,"title":["A parallel and sensitive software tool for methylation analysis on multicore platforms"],"prefix":"10.1093","volume":"31","author":[{"given":"Joaqu\u00edn","family":"T\u00e1rraga","sequence":"first","affiliation":[{"name":"1 Department of Computational Genomics, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariano","family":"P\u00e9rez","sequence":"additional","affiliation":[{"name":"2 Departamento de Inform\u00e1tica, Universidad de Valencia and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan M.","family":"Ordu\u00f1a","sequence":"additional","affiliation":[{"name":"2 Departamento de Inform\u00e1tica, Universidad de Valencia and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9","family":"Duato","sequence":"additional","affiliation":[{"name":"3 DISCA, Universidad Polit\u00e9cnica de Valencia, Valencia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ignacio","family":"Medina","sequence":"additional","affiliation":[{"name":"1 Department of Computational Genomics, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joaqu\u00edn","family":"Dopazo","sequence":"additional","affiliation":[{"name":"1 Department of Computational Genomics, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe,"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,6,10]]},"reference":[{"key":"2023020202310790100_btv357-B1","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/1471-2105-11-203","article-title":"Bs seeker: precise mapping for bisulfite sequencing","volume":"11","author":"Chen","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020202310790100_btv357-B2","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","article-title":"The Sanger FASTQ file format for sequences with quality scores, and the Solexa\/Illumina FASTQ variants","volume":"38","author":"Cock","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023020202310790100_btv357-B3","doi-asserted-by":"crossref","first-page":"3169","DOI":"10.1093\/bioinformatics\/bts605","article-title":"Tools for mapping high-throughput sequencing data","volume":"28","author":"Fonseca","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020202310790100_btv357-B4","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1038\/nrg3230","article-title":"Functions of DNA methylation: islands, start sites, gene bodies and beyond","volume":"13","author":"Jones","year":"2013","journal-title":"Nat. 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Genet."},{"key":"2023020202310790100_btv357-B7","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with burrows-wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020202310790100_btv357-B8","article-title":"Concurrent and accurate RNA sequencing on multicore platforms","volume-title":"Technical report icc 2013-03-01","author":"Mart\u00ednez","year":"2013"},{"key":"2023020202310790100_btv357-B9","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","article-title":"Identification of common molecular subsequences","volume":"147","author":"Smith","year":"1981","journal-title":"J. Mol. 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