CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
Identifieur interne : 001875 ( Main/Exploration ); précédent : 001874; suivant : 001876CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
Auteurs : Rachid Ounit ; Steve Wanamaker ; Timothy J. Close ; Stefano LonardiSource :
- BMC Genomics [ 1471-2164 ] ; 2015.
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Abstract
The problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that modern sequencing technologies can produce.
We introduce
The online version of this article (doi:10.1186/s12864-015-1419-2) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-1419-2
PubMed: 25879410
PubMed Central: 4428112
Affiliations:
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Close</name><affiliation><nlm:aff id="Aff2">Department of Plant & Botanic Sciences, University of California, 900 University Avenue, CA, 92521 Riverside USA</nlm:aff><wicri:noCountry code="subfield">92521 Riverside USA</wicri:noCountry></affiliation></author><author><name sortKey="Lonardi, Stefano" sort="Lonardi, Stefano" uniqKey="Lonardi S" first="Stefano" last="Lonardi">Stefano Lonardi</name><affiliation><nlm:aff id="Aff1">Department of Computer Science & Engineering, University of California, 900 University Avenue, CA, 92521 Riverside USA</nlm:aff><wicri:noCountry code="subfield">92521 Riverside USA</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Genomics</term><term>Internet</term><term>Metagenomics</term><term>User-Computer Interface</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Génomique</term><term>Interface utilisateur</term><term>Internet</term><term>Métagénomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Genomics</term><term>Internet</term><term>Metagenomics</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Génomique</term><term>Interface utilisateur</term><term>Internet</term><term>Métagénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that modern sequencing technologies can produce.</p></sec><sec><title>Results</title><p>We introduce <sc>Clark</sc> a novel approach to classify metagenomic reads at the species or genus level with high accuracy and high speed. Extensive experimental results on various metagenomic samples show that the classification accuracy of <sc>Clark</sc> is better or comparable to the best state-of-the-art tools and it is significantly faster than any of its competitors. In its fastest single-threaded mode <sc>Clark</sc> classifies, with high accuracy, about 32 million metagenomic short reads per minute. <sc>Clark</sc> can also classify BAC clones or transcripts to chromosome arms and centromeric regions.</p></sec><sec><title>Conclusions</title><p><sc>Clark</sc> is a versatile, fast and accurate sequence classification method, especially useful for metagenomics and genomics applications. It is freely available at <ext-link ext-link-type="uri" xlink:href="http://clark.cs.ucr.edu/">http://clark.cs.ucr.edu/</ext-link>.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-1419-2) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Venter, Jc" uniqKey="Venter J">JC Venter</name></author><author><name sortKey="Remington, K" uniqKey="Remington K">K Remington</name></author><author><name sortKey="Heidelberg, Jf" uniqKey="Heidelberg J">JF Heidelberg</name></author><author><name sortKey="Halpern, Al" uniqKey="Halpern A">AL Halpern</name></author><author><name sortKey="Rusch, D" uniqKey="Rusch D">D Rusch</name></author><author><name sortKey="Eisen, Ja" uniqKey="Eisen J">JA Eisen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huttenhower, C" 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uniqKey="Salzberg S">S Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, B" uniqKey="Liu B">B Liu</name></author><author><name sortKey="Gibbons, T" uniqKey="Gibbons T">T Gibbons</name></author><author><name sortKey="Ghodsi, M" uniqKey="Ghodsi M">M Ghodsi</name></author><author><name sortKey="Treangen, T" uniqKey="Treangen T">T Treangen</name></author><author><name sortKey="Pop, M" uniqKey="Pop M">M Pop</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Segata, N" uniqKey="Segata N">N Segata</name></author><author><name sortKey="Waldron, L" uniqKey="Waldron L">L Waldron</name></author><author><name sortKey="Ballarini, A" uniqKey="Ballarini A">A Ballarini</name></author><author><name sortKey="Narasimhan, V" uniqKey="Narasimhan V">V Narasimhan</name></author><author><name sortKey="Jousson, O" uniqKey="Jousson O">O Jousson</name></author><author><name sortKey="Huttenhower, C" uniqKey="Huttenhower C">C Huttenhower</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rosen, Gl" uniqKey="Rosen G">GL Rosen</name></author><author><name sortKey="Reichenberger, Er" uniqKey="Reichenberger E">ER Reichenberger</name></author><author><name sortKey="Rosenfeld, Am" uniqKey="Rosenfeld A">AM Rosenfeld</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Patil, Kr" uniqKey="Patil K">KR Patil</name></author><author><name sortKey="Haider, P" uniqKey="Haider P">P Haider</name></author><author><name sortKey="Pope, Pb" uniqKey="Pope P">PB Pope</name></author><author><name sortKey="Turnbaugh, Pj" uniqKey="Turnbaugh P">PJ Turnbaugh</name></author><author><name sortKey="Morrison, M" uniqKey="Morrison M">M Morrison</name></author><author><name sortKey="Scheffer, T" uniqKey="Scheffer T">T Scheffer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ames, Sk" uniqKey="Ames S">SK Ames</name></author><author><name sortKey="Hysom, Da" uniqKey="Hysom D">DA Hysom</name></author><author><name sortKey="Gardner, Sn" uniqKey="Gardner S">SN Gardner</name></author><author><name sortKey="Lloyd, Gs" uniqKey="Lloyd G">GS Lloyd</name></author><author><name sortKey="Gokhale, Mb" uniqKey="Gokhale M">MB Gokhale</name></author><author><name sortKey="Allen, Je" uniqKey="Allen J">JE Allen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wood, D" uniqKey="Wood D">D Wood</name></author><author><name sortKey="Salzberg, S" uniqKey="Salzberg S">S Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bazinet, Al" uniqKey="Bazinet A">AL Bazinet</name></author><author><name sortKey="Cummings, Mp" uniqKey="Cummings M">MP Cummings</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Koslicki, D" uniqKey="Koslicki D">D Koslicki</name></author><author><name sortKey="Foucart, S" uniqKey="Foucart S">S Foucart</name></author><author><name sortKey="Rosen, G" uniqKey="Rosen G">G Rosen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kent, Wj" uniqKey="Kent W">WJ Kent</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Vinga, S" uniqKey="Vinga S">S Vinga</name></author><author><name sortKey="Almeida, J" uniqKey="Almeida J">J Almeida</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mavromatis, K" uniqKey="Mavromatis K">K Mavromatis</name></author><author><name sortKey="Ivanova, N" uniqKey="Ivanova N">N Ivanova</name></author><author><name sortKey="Barry, K" uniqKey="Barry K">K Barry</name></author><author><name sortKey="Shapiro, H" uniqKey="Shapiro H">H Shapiro</name></author><author><name sortKey="Goltsman, E" uniqKey="Goltsman E">E Goltsman</name></author><author><name sortKey="Mchardy, Ac" uniqKey="Mchardy A">AC McHardy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Magoc, T" uniqKey="Magoc T">T Magoc</name></author><author><name sortKey="Pabinger, S" uniqKey="Pabinger S">S Pabinger</name></author><author><name sortKey="Canzar, S" uniqKey="Canzar S">S Canzar</name></author><author><name sortKey="Liu, X" uniqKey="Liu X">X Liu</name></author><author><name sortKey="Su, Q" uniqKey="Su Q">Q Su</name></author><author><name sortKey="Puiu, D" uniqKey="Puiu D">D Puiu</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Antonio, Ma" uniqKey="Antonio M">MA Antonio</name></author><author><name sortKey="Hawes, Se" uniqKey="Hawes S">SE Hawes</name></author><author><name sortKey="Hillier, Sl" uniqKey="Hillier S">SL Hillier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hyman, Rw" uniqKey="Hyman R">RW Hyman</name></author><author><name sortKey="Fukushima, M" uniqKey="Fukushima M">M Fukushima</name></author><author><name sortKey="Diamond, L" uniqKey="Diamond L">L Diamond</name></author><author><name sortKey="Kumm, J" uniqKey="Kumm J">J Kumm</name></author><author><name sortKey="Giudice, Lc" uniqKey="Giudice L">LC Giudice</name></author><author><name sortKey="Davis, Rw" uniqKey="Davis R">RW Davis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dolezel, J" uniqKey="Dolezel J">J Doležel</name></author><author><name sortKey="Vrana, J" uniqKey="Vrana J">J Vrána</name></author><author><name sortKey="Safa, J" uniqKey="Safa J">J Šafář</name></author><author><name sortKey="Bartos, J" uniqKey="Bartos J">J Bartoš</name></author><author><name sortKey="Kubalakova, M" uniqKey="Kubalakova M">M Kubaláková</name></author><author><name sortKey="Simkova, H" uniqKey="Simkova H">H Šimková</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lonardi, S" uniqKey="Lonardi S">S Lonardi</name></author><author><name sortKey="Duma, D" uniqKey="Duma D">D Duma</name></author><author><name sortKey="Alpert, M" uniqKey="Alpert M">M Alpert</name></author><author><name sortKey="Cordero, F" uniqKey="Cordero F">F Cordero</name></author><author><name sortKey="Beccuti, M" uniqKey="Beccuti M">M Beccuti</name></author><author><name sortKey="Bhat, Pr" uniqKey="Bhat P">PR Bhat</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Luo, R" uniqKey="Luo R">R Luo</name></author><author><name sortKey="Liu, B" uniqKey="Liu B">B Liu</name></author><author><name sortKey="Xie, Y" uniqKey="Xie Y">Y Xie</name></author><author><name sortKey="Li, Z" uniqKey="Li Z">Z Li</name></author><author><name sortKey="Huang, W" uniqKey="Huang W">W Huang</name></author><author><name sortKey="Yuan, J" uniqKey="Yuan J">J Yuan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Close, Tj" uniqKey="Close T">TJ Close</name></author><author><name sortKey="Wanamaker, S" uniqKey="Wanamaker S">S Wanamaker</name></author><author><name sortKey="Roose, Ml" uniqKey="Roose M">ML Roose</name></author><author><name sortKey="Lyon, M" uniqKey="Lyon M">M Lyon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Close, Tj" uniqKey="Close T">TJ Close</name></author><author><name sortKey="Bhat, Pr" uniqKey="Bhat P">PR Bhat</name></author><author><name sortKey="Lonardi, S" uniqKey="Lonardi S">S Lonardi</name></author><author><name sortKey="Wu, Y" uniqKey="Wu Y">Y Wu</name></author><author><name sortKey="Rostoks, N" uniqKey="Rostoks N">N Rostoks</name></author><author><name sortKey="Ramsay, L" uniqKey="Ramsay L">L Ramsay</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mascher, M" uniqKey="Mascher M">M Mascher</name></author><author><name sortKey="Muehlbauer, Gj" uniqKey="Muehlbauer G">GJ Muehlbauer</name></author><author><name sortKey="Rokhsar, Ds" uniqKey="Rokhsar D">DS Rokhsar</name></author><author><name sortKey="Chapman, J" uniqKey="Chapman J">J Chapman</name></author><author><name sortKey="Schmutz, J" uniqKey="Schmutz J">J Schmutz</name></author><author><name sortKey="Barry, K" uniqKey="Barry K">K Barry</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tu, Q" uniqKey="Tu Q">Q Tu</name></author><author><name sortKey="He, Z" uniqKey="He Z">Z He</name></author><author><name sortKey="Zhou, J" uniqKey="Zhou J">J Zhou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Schwartz, S" uniqKey="Schwartz S">S Schwartz</name></author><author><name sortKey="Wagner, L" uniqKey="Wagner L">L Wagner</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Close, Timothy J" sort="Close, Timothy J" uniqKey="Close T" first="Timothy J" last="Close">Timothy J. Close</name><name sortKey="Lonardi, Stefano" sort="Lonardi, Stefano" uniqKey="Lonardi S" first="Stefano" last="Lonardi">Stefano Lonardi</name><name sortKey="Ounit, Rachid" sort="Ounit, Rachid" uniqKey="Ounit R" first="Rachid" last="Ounit">Rachid Ounit</name><name sortKey="Wanamaker, Steve" sort="Wanamaker, Steve" uniqKey="Wanamaker S" first="Steve" last="Wanamaker">Steve Wanamaker</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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