A Parallel Programming Framework for Multi-core DNA Sequence Alignment
A new parallel programming framework for DNA sequence alignment in homogeneous multi-core processor architectures is proposed. Contrasting with traditional coarse-grained parallel approaches, that divide the considered database in several smaller subsets of complete sequences to be aligned with the...
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| creator | de Almeida, Tiago Jose Barreiros Martins Roma, Nuno Filipe Valentim |
| description | A new parallel programming framework for DNA sequence alignment in homogeneous multi-core processor architectures is proposed. Contrasting with traditional coarse-grained parallel approaches, that divide the considered database in several smaller subsets of complete sequences to be aligned with the query sequence, the presented methodology is based on a slicing procedure of both the query and the database sequence under consideration in several tiles/chunks that are concurrently processed by the several cores available in the multi-core processor. The obtained experimental results have proven that significant accelerations of traditional biological sequence alignment algorithms can be obtained, reaching a speedup that is linear with the number of available processing cores and very close to the theoretical maximum. |
| doi_str_mv | 10.1109/CISIS.2010.100 |
| format | Conference Proceeding |
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The obtained experimental results have proven that significant accelerations of traditional biological sequence alignment algorithms can be obtained, reaching a speedup that is linear with the number of available processing cores and very close to the theoretical maximum.</description><subject>Acceleration</subject><subject>Biology computing</subject><subject>Computational biology framework</subject><subject>Concurrent computing</subject><subject>Costs</subject><subject>DNA</subject><subject>Multi-core processor</subject><subject>Multicore processing</subject><subject>Parallel processing</subject><subject>Parallel programming</subject><subject>Sequences</subject><isbn>1424459176</isbn><isbn>9781424459179</isbn><isbn>9780769539676</isbn><isbn>076953967X</isbn><isbn>9781424459186</isbn><isbn>1424459184</isbn><fulltext>true</fulltext><rsrctype>conference_proceeding</rsrctype><creationdate>2010</creationdate><recordtype>conference_proceeding</recordtype><sourceid>6IE</sourceid><sourceid>RIE</sourceid><recordid>eNotjLtOwzAARY0QElCysrD4B1L8foxRICVSgUqBuXJsJzI4CTipEH9PEdzlnLNcAK4xWmOM9G1ZN3WzJui3EToBmZYKSaE51UKKU3CJGWGMayzFOcjm-Q0dxzghlFyAqoA7k0yMPsJdmvpkhiGMPayO4r-m9A67KcHHQ1xCbqfk4d1TARv_efCj9bCIoR8HPy5X4KwzcfbZP1fgtbp_KR_y7fOmLottHrDkS25sK1irHTaIKSUEtVZaqajonHdEGkOd4a7jSnNHtbW4ddI6yjtEtaLY0RW4-fsN3vv9RwqDSd97zphkitAf7k1MCg</recordid><startdate>201002</startdate><enddate>201002</enddate><creator>de Almeida, Tiago Jose Barreiros Martins</creator><creator>Roma, Nuno Filipe Valentim</creator><general>IEEE</general><scope>6IE</scope><scope>6IL</scope><scope>CBEJK</scope><scope>RIE</scope><scope>RIL</scope></search><sort><creationdate>201002</creationdate><title>A Parallel Programming Framework for Multi-core DNA Sequence Alignment</title><author>de Almeida, Tiago Jose Barreiros Martins ; Roma, Nuno Filipe Valentim</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-i175t-acb64b9d1a0488663cc7c7836fded27aa3da5df5895d39cc1bd7cd35f039831d3</frbrgroupid><rsrctype>conference_proceedings</rsrctype><prefilter>conference_proceedings</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Acceleration</topic><topic>Biology computing</topic><topic>Computational biology framework</topic><topic>Concurrent computing</topic><topic>Costs</topic><topic>DNA</topic><topic>Multi-core processor</topic><topic>Multicore processing</topic><topic>Parallel processing</topic><topic>Parallel programming</topic><topic>Sequences</topic><toplevel>online_resources</toplevel><creatorcontrib>de Almeida, Tiago Jose Barreiros Martins</creatorcontrib><creatorcontrib>Roma, Nuno Filipe Valentim</creatorcontrib><collection>IEEE Electronic Library (IEL) Conference Proceedings</collection><collection>IEEE Proceedings Order Plan All Online (POP All Online) 1998-present by volume</collection><collection>IEEE Xplore All Conference Proceedings</collection><collection>IEEE Electronic Library (IEL)</collection><collection>IEEE Proceedings Order Plans (POP All) 1998-Present</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>de Almeida, Tiago Jose Barreiros Martins</au><au>Roma, Nuno Filipe Valentim</au><format>book</format><genre>proceeding</genre><ristype>CONF</ristype><atitle>A Parallel Programming Framework for Multi-core DNA Sequence Alignment</atitle><btitle>2010 International Conference on Complex, Intelligent and Software Intensive Systems</btitle><stitle>CISIS</stitle><date>2010-02</date><risdate>2010</risdate><spage>907</spage><epage>912</epage><pages>907-912</pages><isbn>1424459176</isbn><isbn>9781424459179</isbn><eisbn>9780769539676</eisbn><eisbn>076953967X</eisbn><eisbn>9781424459186</eisbn><eisbn>1424459184</eisbn><abstract>A new parallel programming framework for DNA sequence alignment in homogeneous multi-core processor architectures is proposed. Contrasting with traditional coarse-grained parallel approaches, that divide the considered database in several smaller subsets of complete sequences to be aligned with the query sequence, the presented methodology is based on a slicing procedure of both the query and the database sequence under consideration in several tiles/chunks that are concurrently processed by the several cores available in the multi-core processor. The obtained experimental results have proven that significant accelerations of traditional biological sequence alignment algorithms can be obtained, reaching a speedup that is linear with the number of available processing cores and very close to the theoretical maximum.</abstract><pub>IEEE</pub><doi>10.1109/CISIS.2010.100</doi><tpages>6</tpages></addata></record> |
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| subjects | Acceleration Biology computing Computational biology framework Concurrent computing Costs DNA Multi-core processor Multicore processing Parallel processing Parallel programming Sequences |
| title | A Parallel Programming Framework for Multi-core DNA Sequence Alignment |
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