{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T12:37:07Z","timestamp":1740141427559,"version":"3.37.3"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2020,9,9]],"date-time":"2020-09-09T00:00:00Z","timestamp":1599609600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100006730","name":"Ministry of Education and Research, Romania","doi-asserted-by":"publisher","award":["28PFE"],"award-info":[{"award-number":["28PFE"]}],"id":[{"id":"10.13039\/501100006730","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Decoding the human genome in the past decades has brought into focus a computationally intensive operation through DNA profiling. The typical search space for these kinds of problems is extremely large and requires specialized hardware and algorithms to perform the necessary sequence analysis. In this paper, we propose an innovative and scalable approach to exact multi-pattern matching of nucleotide sequences by harnessing the massively parallel computing power found in commodity graphical processing units. Our approach places careful consideration on preprocessing of DNA datasets and runtime performance, while exploiting the full capabilities of the heterogeneous platform it runs on. Finally, we evaluate our models against real-world DNA sequences.<\/jats:p>","DOI":"10.1093\/jigpal\/jzaa034","type":"journal-article","created":{"date-parts":[[2020,8,6]],"date-time":"2020-08-06T19:31:59Z","timestamp":1596742319000},"page":"906-924","source":"Crossref","is-referenced-by-count":2,"title":["Towards real-time DNA biometrics using GPU-accelerated processing"],"prefix":"10.1093","volume":"29","author":[{"given":"Mario","family":"Reja","sequence":"first","affiliation":[{"name":"Faculty of Mathematics and Informatics, West University of Timisoara, Timis county, Timisoara 300223, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ciprian","family":"Pungila","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics and Informatics, West University of Timisoara, Timis county, Timisoara 300223, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Viorel","family":"Negru","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics and Informatics, West University of Timisoara, Timis county, Timisoara 300223, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,9,9]]},"reference":[{"article-title":"Gpu accelerated pattern matching algorithm for DNA sequences to detect cancer using CUDA dissertation","year":"2013","author":"Adey","key":"2021111806233255300_ref1"},{"key":"2021111806233255300_ref2","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1145\/360825.360855","article-title":"Efficient string matching: an aid to bibliographic search","volume":"18","author":"Aho","year":"1975","journal-title":"Communications of the ACM"},{"key":"2021111806233255300_ref3","first-page":"51","article-title":"Chapter 2\u2014CUDA programming model","volume-title":"Professional CUDA C Programming","author":"Cheng","year":"2014"},{"key":"2021111806233255300_ref4","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1007\/3-540-09510-1_10","article-title":"A string matching algorithm fast on the average","volume-title":"Automata, Languages and Programming","author":"Commentz-Walter","year":"1979"},{"key":"2021111806233255300_ref5","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1038\/nature03001","article-title":"Finishing the euchromatic sequence of the human genome","volume":"431","author":"International Human Genome Sequencing Consortium","year":"2004","journal-title":"Nature"},{"key":"2021111806233255300_ref6","article-title":"A single DNA difference in the HERC2 gene explains blue eyes","volume-title":"Genetics in the News","author":"Cunningham","year":"2008"},{"key":"2021111806233255300_ref7","first-page":"85","article-title":"Chapter 4\u2014the CUDA execution model","volume-title":"CUDA Application Design and Development","author":"Farber","year":"2011"},{"article-title":"The Microarchitecture of intel, AMD and VIA CPUs. 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