WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures
Identifieur interne : 000038 ( France/Analysis ); précédent : 000037; suivant : 000039WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures
Auteurs : Jens Lichtenberg [États-Unis] ; Kyle Kurz [États-Unis] ; Xiaoyu Liang [États-Unis] ; Rami Al-Ouran [États-Unis] ; Lev Neiman [États-Unis] ; Lee J. Nau [États-Unis] ; Joshua D. Welch [États-Unis] ; Edwin Jacox [France] ; Thomas Bitterman [États-Unis] ; Klaus Ecker [États-Unis] ; Laura Elnitski [États-Unis] ; Frank Drews [États-Unis] ; Stephen Sauchi Lee [États-Unis] ; Lonnie R. Welch [États-Unis]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2010.
Abstract
An important focus of genomic science is the discovery and characterization of all functional elements within genomes.
This manuscript presents WordSeeker, an enumerative motif discovery toolkit that utilizes multi-core and distributed computational platforms to enable scalable analysis of genomic data. A controller task coordinates activities of worker nodes, each of which (1) enumerates a subset of the DNA
A comprehensive suite of performance tests was conducted to demonstrate the performance, speedup and efficiency of WordSeeker. The scalability of the toolkit enabled the analysis of the entire genome of
WordSeeker effectively utilizes concurrent computing platforms to enable the identification of putative functional elements in genomic data sets. This capability facilitates the analysis of the large quantity of sequenced genomic data.
Url:
DOI: 10.1186/1471-2105-11-S12-S6
PubMed: 21210985
PubMed Central: 3040532
Affiliations:
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Nau</name><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701</wicri:regionArea><wicri:noRegion>Ohio 45701</wicri:noRegion></affiliation></author><author><name sortKey="Welch, Joshua D" sort="Welch, Joshua D" uniqKey="Welch J" first="Joshua D" last="Welch">Joshua D. Welch</name><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701</wicri:regionArea><wicri:noRegion>Ohio 45701</wicri:noRegion></affiliation></author><author><name sortKey="Jacox, Edwin" sort="Jacox, Edwin" uniqKey="Jacox E" first="Edwin" last="Jacox">Edwin Jacox</name><affiliation wicri:level="3"><nlm:aff id="I2">Developmental Biology Institute of Marseille, Luminy F-13009, Marseille, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Developmental Biology Institute of Marseille, Luminy F-13009, Marseille</wicri:regionArea><placeName><region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region><settlement type="city">Marseille</settlement></placeName></affiliation></author><author><name sortKey="Bitterman, Thomas" sort="Bitterman, Thomas" uniqKey="Bitterman T" first="Thomas" last="Bitterman">Thomas Bitterman</name><affiliation wicri:level="1"><nlm:aff id="I3">Cyberinfrastructure Group, Ohio Supercomputer Center, Columbus, Ohio 43212, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cyberinfrastructure Group, Ohio Supercomputer Center, Columbus, Ohio 43212</wicri:regionArea><wicri:noRegion>Ohio 43212</wicri:noRegion></affiliation></author><author><name sortKey="Ecker, Klaus" sort="Ecker, Klaus" uniqKey="Ecker K" first="Klaus" last="Ecker">Klaus Ecker</name><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701</wicri:regionArea><wicri:noRegion>Ohio 45701</wicri:noRegion></affiliation></author><author><name sortKey="Elnitski, Laura" sort="Elnitski, Laura" uniqKey="Elnitski L" first="Laura" last="Elnitski">Laura Elnitski</name><affiliation wicri:level="2"><nlm:aff id="I4">Genomic Functional Analysis Section, National Human Genome Research Institute, NIH, Rockville, Maryland 20892 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Genomic Functional Analysis Section, National Human Genome Research Institute, NIH, Rockville</wicri:cityArea></affiliation></author><author><name sortKey="Drews, Frank" sort="Drews, Frank" uniqKey="Drews F" first="Frank" last="Drews">Frank Drews</name><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701</wicri:regionArea><wicri:noRegion>Ohio 45701</wicri:noRegion></affiliation></author><author><name sortKey="Lee, Stephen Sauchi" sort="Lee, Stephen Sauchi" uniqKey="Lee S" first="Stephen Sauchi" last="Lee">Stephen Sauchi Lee</name><affiliation wicri:level="1"><nlm:aff id="I5">Department of Statistics, University of Idaho, Moscow, Idaho 83844, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Statistics, University of Idaho, Moscow, Idaho 83844</wicri:regionArea><wicri:noRegion>Idaho 83844</wicri:noRegion></affiliation></author><author><name sortKey="Welch, Lonnie R" sort="Welch, Lonnie R" uniqKey="Welch L" first="Lonnie R" last="Welch">Lonnie R. Welch</name><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701</wicri:regionArea><wicri:noRegion>Ohio 45701</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I6">Biomedical Engineering Program, Ohio University, Athens, Ohio 45701, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biomedical Engineering Program, Ohio University, Athens, Ohio 45701</wicri:regionArea><wicri:noRegion>Ohio 45701</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I7">Molecular and Cellular Biology Program, Ohio University, Athens, Ohio 45701, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Molecular and Cellular Biology Program, Ohio University, Athens, Ohio 45701</wicri:regionArea><wicri:noRegion>Ohio 45701</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>An important focus of genomic science is the discovery and characterization of all functional elements within genomes. <italic>In silico</italic> methods are used in genome studies to discover putative regulatory genomic elements (called words or motifs). Although a number of methods have been developed for motif discovery, most of them lack the scalability needed to analyze large genomic data sets.</p></sec><sec><title>Methods</title><p>This manuscript presents WordSeeker, an enumerative motif discovery toolkit that utilizes multi-core and distributed computational platforms to enable scalable analysis of genomic data. A controller task coordinates activities of worker nodes, each of which (1) enumerates a subset of the DNA <italic>word space</italic> and (2) scores words with a distributed Markov chain model.</p></sec><sec><title>Results</title><p>A comprehensive suite of performance tests was conducted to demonstrate the performance, speedup and efficiency of WordSeeker. The scalability of the toolkit enabled the analysis of the entire genome of <italic>Arabidopsis thaliana</italic>; the results of the analysis were integrated into The Arabidopsis Gene Regulatory Information Server (AGRIS). A public version of WordSeeker was deployed on the Glenn cluster at the Ohio Supercomputer Center.</p></sec><sec><title>Conclusion</title><p>WordSeeker effectively utilizes concurrent computing platforms to enable the identification of putative functional elements in genomic data sets. This capability facilitates the analysis of the large quantity of sequenced genomic data.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Blahnik, Kr" uniqKey="Blahnik K">KR Blahnik</name></author><author><name sortKey="Dou, L" uniqKey="Dou L">L Dou</name></author><author><name sortKey="O Geen, H" uniqKey="O Geen H">H O'Geen</name></author><author><name sortKey="Mcphillips, T" uniqKey="Mcphillips T">T McPhillips</name></author><author><name sortKey="Xu, X" uniqKey="Xu X">X Xu</name></author><author><name sortKey="Cao, Ar" uniqKey="Cao A">AR Cao</name></author><author><name sortKey="Iyengar, S" uniqKey="Iyengar S">S Iyengar</name></author><author><name sortKey="Nicolet, Cm" uniqKey="Nicolet C">CM Nicolet</name></author><author><name sortKey="Ludascher, B" uniqKey="Ludascher B">B Ludascher</name></author><author><name sortKey="Korf, I" uniqKey="Korf I">I Korf</name></author><author><name 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sortKey="Welch, J" uniqKey="Welch J">J Welch</name></author><author><name sortKey="Kurz, K" uniqKey="Kurz K">K Kurz</name></author><author><name sortKey="Liang, X" uniqKey="Liang X">X Liang</name></author><author><name sortKey="Yang, M" uniqKey="Yang M">M Yang</name></author><author><name sortKey="Drews, F" uniqKey="Drews F">F Drews</name></author><author><name sortKey="Ecker, K" uniqKey="Ecker K">K Ecker</name></author><author><name sortKey="Lee, S" uniqKey="Lee S">S Lee</name></author><author><name sortKey="Elnitski, L" uniqKey="Elnitski L">L Elnitski</name></author><author><name sortKey="Welch, L" uniqKey="Welch L">L Welch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lichtenberg, J" uniqKey="Lichtenberg J">J Lichtenberg</name></author><author><name sortKey="Yilmaz, A" uniqKey="Yilmaz A">A Yilmaz</name></author><author><name sortKey="Welch, J" uniqKey="Welch J">J Welch</name></author><author><name sortKey="Kurz, K" uniqKey="Kurz K">K Kurz</name></author><author><name sortKey="Liang, X" uniqKey="Liang X">X Liang</name></author><author><name sortKey="Drews, F" uniqKey="Drews F">F Drews</name></author><author><name sortKey="Ecker, K" uniqKey="Ecker K">K Ecker</name></author><author><name sortKey="Lee, S" uniqKey="Lee S">S Lee</name></author><author><name sortKey="Geisler, M" uniqKey="Geisler M">M Geisler</name></author><author><name sortKey="Grotewold, E" uniqKey="Grotewold E">E Grotewold</name></author><author><name sortKey="Welch, L" uniqKey="Welch L">L Welch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liang, X" uniqKey="Liang X">X Liang</name></author><author><name sortKey="Shen, K" uniqKey="Shen K">K Shen</name></author><author><name sortKey="Lichtenberg, J" uniqKey="Lichtenberg J">J Lichtenberg</name></author><author><name sortKey="Wyatt, Se" uniqKey="Wyatt S">SE Wyatt</name></author><author><name sortKey="Welch, Lr" uniqKey="Welch L">LR Welch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lichtenberg, J" uniqKey="Lichtenberg J">J Lichtenberg</name></author><author><name sortKey="Yilmaz, A" uniqKey="Yilmaz A">A Yilmaz</name></author><author><name sortKey="Kurz, K" uniqKey="Kurz K">K Kurz</name></author><author><name sortKey="Liang, X" uniqKey="Liang X">X Liang</name></author><author><name sortKey="Nelson, C" uniqKey="Nelson C">C Nelson</name></author><author><name sortKey="Bitterman, T" uniqKey="Bitterman T">T Bitterman</name></author><author><name sortKey="Stockinger, E" uniqKey="Stockinger E">E Stockinger</name></author><author><name sortKey="Grotewold, E" uniqKey="Grotewold E">E Grotewold</name></author><author><name sortKey="Welch, Lr" uniqKey="Welch L">LR Welch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Davaluri, Rv" uniqKey="Davaluri R">RV Davaluri</name></author><author><name sortKey="Sun, H" uniqKey="Sun H">H Sun</name></author><author><name sortKey="Palaniswamy, Sk" uniqKey="Palaniswamy S">SK Palaniswamy</name></author><author><name sortKey="Matthews, N" uniqKey="Matthews N">N Matthews</name></author><author><name sortKey="Molina, C" uniqKey="Molina C">C Molina</name></author><author><name sortKey="Kurtz, M" uniqKey="Kurtz M">M Kurtz</name></author><author><name sortKey="Grotewold, E" uniqKey="Grotewold E">E Grotewold</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kurz, K" uniqKey="Kurz K">K Kurz</name></author><author><name sortKey="Lichtenberg, J" uniqKey="Lichtenberg J">J Lichtenberg</name></author><author><name sortKey="Nau, L" uniqKey="Nau L">L Nau</name></author><author><name sortKey="Drews, F" uniqKey="Drews F">F Drews</name></author><author><name sortKey="Welch, Lr" uniqKey="Welch L">LR Welch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kurz, K" uniqKey="Kurz K">K Kurz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tian, Y" uniqKey="Tian Y">Y Tian</name></author><author><name sortKey="Tata, S" uniqKey="Tata S">S Tata</name></author><author><name sortKey="Hankins, Ra" uniqKey="Hankins R">RA Hankins</name></author><author><name sortKey="Patel, Jm" uniqKey="Patel J">JM Patel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Drews, F" uniqKey="Drews F">F Drews</name></author><author><name sortKey="Lichtenberg, J" uniqKey="Lichtenberg J">J Lichtenberg</name></author><author><name sortKey="Welch, L" uniqKey="Welch L">L Welch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tompa, M" uniqKey="Tompa M">M Tompa</name></author><author><name sortKey="Li, N" uniqKey="Li N">N Li</name></author><author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name></author><author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</name></author><author><name sortKey="De Moor, B" uniqKey="De Moor B">B De Moor</name></author><author><name sortKey="Eskin, E" uniqKey="Eskin E">E Eskin</name></author><author><name sortKey="Favorov, Av" uniqKey="Favorov A">AV Favorov</name></author><author><name sortKey="Frith, Mc" uniqKey="Frith M">MC Frith</name></author><author><name sortKey="Fu, Y" uniqKey="Fu Y">Y Fu</name></author><author><name sortKey="Kent, Wj" uniqKey="Kent W">WJ Kent</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grotewold, E" uniqKey="Grotewold E">E Grotewold</name></author><author><name sortKey="Springer, N" uniqKey="Springer N">N Springer</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>France</li><li>États-Unis</li></country><region><li>Maryland</li><li>Provence-Alpes-Côte d'Azur</li></region><settlement><li>Marseille</li></settlement></list><tree><country name="États-Unis"><noRegion><name sortKey="Lichtenberg, Jens" sort="Lichtenberg, Jens" uniqKey="Lichtenberg J" first="Jens" last="Lichtenberg">Jens Lichtenberg</name></noRegion><name sortKey="Al Ouran, Rami" sort="Al Ouran, Rami" uniqKey="Al Ouran R" first="Rami" last="Al-Ouran">Rami Al-Ouran</name><name sortKey="Bitterman, Thomas" sort="Bitterman, Thomas" uniqKey="Bitterman T" first="Thomas" last="Bitterman">Thomas Bitterman</name><name sortKey="Drews, Frank" sort="Drews, Frank" uniqKey="Drews F" first="Frank" last="Drews">Frank Drews</name><name sortKey="Ecker, Klaus" sort="Ecker, Klaus" uniqKey="Ecker K" first="Klaus" last="Ecker">Klaus Ecker</name><name sortKey="Elnitski, Laura" sort="Elnitski, Laura" uniqKey="Elnitski L" first="Laura" last="Elnitski">Laura Elnitski</name><name sortKey="Kurz, Kyle" sort="Kurz, Kyle" uniqKey="Kurz K" first="Kyle" last="Kurz">Kyle Kurz</name><name sortKey="Lee, Stephen Sauchi" sort="Lee, Stephen Sauchi" uniqKey="Lee S" first="Stephen Sauchi" last="Lee">Stephen Sauchi Lee</name><name sortKey="Liang, Xiaoyu" sort="Liang, Xiaoyu" uniqKey="Liang X" first="Xiaoyu" last="Liang">Xiaoyu Liang</name><name sortKey="Nau, Lee J" sort="Nau, Lee J" uniqKey="Nau L" first="Lee J" last="Nau">Lee J. Nau</name><name sortKey="Neiman, Lev" sort="Neiman, Lev" uniqKey="Neiman L" first="Lev" last="Neiman">Lev Neiman</name><name sortKey="Welch, Joshua D" sort="Welch, Joshua D" uniqKey="Welch J" first="Joshua D" last="Welch">Joshua D. Welch</name><name sortKey="Welch, Lonnie R" sort="Welch, Lonnie R" uniqKey="Welch L" first="Lonnie R" last="Welch">Lonnie R. Welch</name><name sortKey="Welch, Lonnie R" sort="Welch, Lonnie R" uniqKey="Welch L" first="Lonnie R" last="Welch">Lonnie R. Welch</name><name sortKey="Welch, Lonnie R" sort="Welch, Lonnie R" uniqKey="Welch L" first="Lonnie R" last="Welch">Lonnie R. Welch</name></country><country name="France"><region name="Provence-Alpes-Côte d'Azur"><name sortKey="Jacox, Edwin" sort="Jacox, Edwin" uniqKey="Jacox E" first="Edwin" last="Jacox">Edwin Jacox</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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