An Efficient Parallel Algorithm for Multiple Sequence Similarities Calculation Using a Low Complexity Method
Identifieur interne : 001D50 ( Main/Exploration ); précédent : 001D49; suivant : 001D51An Efficient Parallel Algorithm for Multiple Sequence Similarities Calculation Using a Low Complexity Method
Auteurs : Evandro A. Marucci [Brésil] ; Geraldo F. D. Zafalon [Brésil] ; Julio C. Momente [Brésil] ; Leandro A. Neves [Brésil] ; Carlo R. Valêncio [Brésil] ; Alex R. Pinto [Brésil] ; Adriano M. Cansian [Brésil] ; Rogeria C. G. De Souza [Brésil] ; Yang Shiyou [République populaire de Chine] ; José M. Machado [Brésil]Source :
- BioMed Research International [ 2314-6133 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- methods : Computational Biology.
- Algorithms, Genome, Sequence Alignment, Sequence Homology, Software.
Abstract
With the advance of genomic researches, the number of sequences involved in comparative methods has grown immensely. Among them, there are methods for similarities calculation, which are used by many bioinformatics applications. Due the huge amount of data, the union of low complexity methods with the use of parallel computing is becoming desirable. The
Url:
DOI: 10.1155/2014/563016
PubMed: 25140318
PubMed Central: 4130029
Affiliations:
- Brésil, République populaire de Chine
- Santa Catarina, Zhejiang, État de São Paulo
- Hangzhou
- Université de Zhejiang
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Machado</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP</wicri:regionArea><placeName><region type="state">État de São Paulo</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25140318</idno><idno type="pmc">4130029</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4130029</idno><idno type="RBID">PMC:4130029</idno><idno type="doi">10.1155/2014/563016</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000B31</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000B31</idno><idno type="wicri:Area/Pmc/Curation">000B31</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000B31</idno><idno type="wicri:Area/Pmc/Checkpoint">001142</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001142</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:25140318</idno><idno type="wicri:Area/PubMed/Corpus">001876</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001876</idno><idno type="wicri:Area/PubMed/Curation">001876</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001876</idno><idno type="wicri:Area/PubMed/Checkpoint">001999</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001999</idno><idno type="wicri:Area/Ncbi/Merge">000E71</idno><idno type="wicri:Area/Ncbi/Curation">000E71</idno><idno type="wicri:Area/Ncbi/Checkpoint">000E71</idno><idno type="wicri:doubleKey">2314-6133:2014:Marucci E:an:efficient:parallel</idno><idno type="wicri:Area/Main/Merge">001D65</idno><idno type="wicri:Area/Main/Curation">001D50</idno><idno type="wicri:Area/Main/Exploration">001D50</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">An Efficient Parallel Algorithm for Multiple Sequence Similarities Calculation Using a Low Complexity Method</title><author><name sortKey="Marucci, Evandro A" sort="Marucci, Evandro A" uniqKey="Marucci E" first="Evandro A." last="Marucci">Evandro A. Marucci</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP</wicri:regionArea><placeName><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Zafalon, Geraldo F D" sort="Zafalon, Geraldo F D" uniqKey="Zafalon G" first="Geraldo F. D." last="Zafalon">Geraldo F. D. Zafalon</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP</wicri:regionArea><placeName><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Momente, Julio C" sort="Momente, Julio C" uniqKey="Momente J" first="Julio C." last="Momente">Julio C. Momente</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP</wicri:regionArea><placeName><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Neves, Leandro A" sort="Neves, Leandro A" uniqKey="Neves L" first="Leandro A." last="Neves">Leandro A. Neves</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP</wicri:regionArea><placeName><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Valencio, Carlo R" sort="Valencio, Carlo R" uniqKey="Valencio C" first="Carlo R." last="Valêncio">Carlo R. Valêncio</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP</wicri:regionArea><placeName><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Pinto, Alex R" sort="Pinto, Alex R" uniqKey="Pinto A" first="Alex R." last="Pinto">Alex R. Pinto</name><affiliation wicri:level="2"><nlm:aff id="I2">Department of Control Engineering and Automation, Federal University of Santa Catarina, Rua Pomerode 710, 89065-300 Blumenau, SC, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Control Engineering and Automation, Federal University of Santa Catarina, Rua Pomerode 710, 89065-300 Blumenau, SC</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author><author><name sortKey="Cansian, Adriano M" sort="Cansian, Adriano M" uniqKey="Cansian A" first="Adriano M." last="Cansian">Adriano M. Cansian</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP</wicri:regionArea><placeName><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="De Souza, Rogeria C G" sort="De Souza, Rogeria C G" uniqKey="De Souza R" first="Rogeria C. G." last="De Souza">Rogeria C. G. De Souza</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP</wicri:regionArea><placeName><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Shiyou, Yang" sort="Shiyou, Yang" uniqKey="Shiyou Y" first="Yang" last="Shiyou">Yang Shiyou</name><affiliation wicri:level="4"><nlm:aff id="I3">College of Electrical Engineering, Zhejiang University, Hangzhou 310027, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Electrical Engineering, Zhejiang University, Hangzhou 310027</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName><orgName type="university">Université de Zhejiang</orgName><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Machado, Jose M" sort="Machado, Jose M" uniqKey="Machado J" first="José M." last="Machado">José M. Machado</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP</wicri:regionArea><placeName><region type="state">État de São Paulo</region></placeName></affiliation></author></analytic><series><title level="j">BioMed Research International</title><idno type="ISSN">2314-6133</idno><idno type="eISSN">2314-6141</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Computational Biology (methods)</term><term>Genome</term><term>Sequence Alignment</term><term>Sequence Homology</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Alignement de séquences</term><term>Biologie informatique ()</term><term>Génome</term><term>Logiciel</term><term>Similitude de séquences</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Genome</term><term>Sequence Alignment</term><term>Sequence Homology</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Alignement de séquences</term><term>Biologie informatique</term><term>Génome</term><term>Logiciel</term><term>Similitude de séquences</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>With the advance of genomic researches, the number of sequences involved in comparative methods has grown immensely. Among them, there are methods for similarities calculation, which are used by many bioinformatics applications. Due the huge amount of data, the union of low complexity methods with the use of parallel computing is becoming desirable. The <italic>k-mers</italic> counting is a very efficient method with good biological results. In this work, the development of a parallel algorithm for multiple sequence similarities calculation using the <italic>k-mers</italic> counting method is proposed. Tests show that the algorithm presents a very good scalability and a nearly linear speedup. For 14 nodes was obtained 12x speedup. This algorithm can be used in the parallelization of some multiple sequence alignment tools, such as MAFFT and MUSCLE.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Edgar, Rc" uniqKey="Edgar R">RC Edgar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zafalon, Gf" uniqKey="Zafalon G">GF Zafalon</name></author><author><name sortKey="Marucci, Ea" uniqKey="Marucci E">EA Marucci</name></author><author><name sortKey="Momente, Jc" uniqKey="Momente J">JC Momente</name></author><author><name sortKey="Amazonas, Jr" uniqKey="Amazonas J">JR Amazonas</name></author><author><name sortKey="Sato, Lm" uniqKey="Sato L">LM Sato</name></author><author><name sortKey="Machado, Jm" uniqKey="Machado J">JM Machado</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Deng, X" uniqKey="Deng X">X Deng</name></author><author><name sortKey="Li, E" uniqKey="Li E">E Li</name></author><author><name sortKey="Shan, J" uniqKey="Shan J">J Shan</name></author><author><name sortKey="Chen, W" uniqKey="Chen W">W Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Arcuri, Ha" uniqKey="Arcuri H">HA Arcuri</name></author><author><name sortKey="Zafalon, Gfd" uniqKey="Zafalon G">GFD Zafalon</name></author><author><name sortKey="Marucci, Ea" uniqKey="Marucci E">EA Marucci</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marucci, Ea" uniqKey="Marucci E">EA Marucci</name></author><author><name sortKey="Zafalon, Gf" uniqKey="Zafalon G">GF Zafalon</name></author><author><name sortKey="Momente, Jc" uniqKey="Momente J">JC Momente</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Katoh, K" uniqKey="Katoh K">K Katoh</name></author><author><name sortKey="Misawa, K" uniqKey="Misawa K">K Misawa</name></author><author><name sortKey="Kuma, K" uniqKey="Kuma K">K Kuma</name></author><author><name sortKey="Miyata, T" uniqKey="Miyata T">T Miyata</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Katoh, K" uniqKey="Katoh K">K Katoh</name></author><author><name sortKey="Toh, H" uniqKey="Toh H">H Toh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Edgar, Rc" uniqKey="Edgar R">RC Edgar</name></author><author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Quinn, Mj" uniqKey="Quinn M">MJ Quinn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Edgar, Rc" uniqKey="Edgar R">RC Edgar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Amdahl, Gm" uniqKey="Amdahl G">GM Amdahl</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Brésil</li><li>République populaire de Chine</li></country><region><li>Santa Catarina</li><li>Zhejiang</li><li>État de São Paulo</li></region><settlement><li>Hangzhou</li></settlement><orgName><li>Université de Zhejiang</li></orgName></list><tree><country name="Brésil"><region name="État de São Paulo"><name sortKey="Marucci, Evandro A" sort="Marucci, Evandro A" uniqKey="Marucci E" first="Evandro A." last="Marucci">Evandro A. Marucci</name></region><name sortKey="Cansian, Adriano M" sort="Cansian, Adriano M" uniqKey="Cansian A" first="Adriano M." last="Cansian">Adriano M. Cansian</name><name sortKey="De Souza, Rogeria C G" sort="De Souza, Rogeria C G" uniqKey="De Souza R" first="Rogeria C. G." last="De Souza">Rogeria C. G. De Souza</name><name sortKey="Machado, Jose M" sort="Machado, Jose M" uniqKey="Machado J" first="José M." last="Machado">José M. Machado</name><name sortKey="Momente, Julio C" sort="Momente, Julio C" uniqKey="Momente J" first="Julio C." last="Momente">Julio C. Momente</name><name sortKey="Neves, Leandro A" sort="Neves, Leandro A" uniqKey="Neves L" first="Leandro A." last="Neves">Leandro A. Neves</name><name sortKey="Pinto, Alex R" sort="Pinto, Alex R" uniqKey="Pinto A" first="Alex R." last="Pinto">Alex R. Pinto</name><name sortKey="Valencio, Carlo R" sort="Valencio, Carlo R" uniqKey="Valencio C" first="Carlo R." last="Valêncio">Carlo R. Valêncio</name><name sortKey="Zafalon, Geraldo F D" sort="Zafalon, Geraldo F D" uniqKey="Zafalon G" first="Geraldo F. D." last="Zafalon">Geraldo F. D. Zafalon</name></country><country name="République populaire de Chine"><region name="Zhejiang"><name sortKey="Shiyou, Yang" sort="Shiyou, Yang" uniqKey="Shiyou Y" first="Yang" last="Shiyou">Yang Shiyou</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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