CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
Identifieur interne : 001097 ( Ncbi/Merge ); précédent : 001096; suivant : 001098CLARK: 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.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
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
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000292
- to stream Pmc, to step Curation: 000292
- to stream Pmc, to step Checkpoint: 000F01
- to stream PubMed, to step Corpus: 001644
- to stream PubMed, to step Curation: 001644
- to stream PubMed, to step Checkpoint: 001619
Links to Exploration step
PMC:4428112Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative <italic>k</italic>
-mers</title>
<author><name sortKey="Ounit, Rachid" sort="Ounit, Rachid" uniqKey="Ounit R" first="Rachid" last="Ounit">Rachid Ounit</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>
<author><name sortKey="Wanamaker, Steve" sort="Wanamaker, Steve" uniqKey="Wanamaker S" first="Steve" last="Wanamaker">Steve Wanamaker</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="Close, Timothy J" sort="Close, Timothy J" uniqKey="Close T" first="Timothy J" last="Close">Timothy J. 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>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">25879410</idno>
<idno type="pmc">4428112</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428112</idno>
<idno type="RBID">PMC:4428112</idno>
<idno type="doi">10.1186/s12864-015-1419-2</idno>
<date when="2015">2015</date>
<idno type="wicri:Area/Pmc/Corpus">000292</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000292</idno>
<idno type="wicri:Area/Pmc/Curation">000292</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000292</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000F01</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000F01</idno>
<idno type="wicri:source">PubMed</idno>
<idno type="RBID">pubmed:25879410</idno>
<idno type="wicri:Area/PubMed/Corpus">001644</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001644</idno>
<idno type="wicri:Area/PubMed/Curation">001644</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001644</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001619</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001619</idno>
<idno type="wicri:Area/Ncbi/Merge">001097</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative <italic>k</italic>
-mers</title>
<author><name sortKey="Ounit, Rachid" sort="Ounit, Rachid" uniqKey="Ounit R" first="Rachid" last="Ounit">Rachid Ounit</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>
<author><name sortKey="Wanamaker, Steve" sort="Wanamaker, Steve" uniqKey="Wanamaker S" first="Steve" last="Wanamaker">Steve Wanamaker</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="Close, Timothy J" sort="Close, Timothy J" uniqKey="Close T" first="Timothy J" last="Close">Timothy J. 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" uniqKey="Huttenhower C">C Huttenhower</name>
</author>
<author><name sortKey="Gevers, D" uniqKey="Gevers D">D Gevers</name>
</author>
<author><name sortKey="Knight, R" uniqKey="Knight R">R Knight</name>
</author>
<author><name sortKey="Abubucker, S" uniqKey="Abubucker S">S Abubucker</name>
</author>
<author><name sortKey="Badger, Jh" uniqKey="Badger J">JH Badger</name>
</author>
<author><name sortKey="Chinwalla, At" uniqKey="Chinwalla A">AT Chinwalla</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Huson, Dh" uniqKey="Huson D">DH Huson</name>
</author>
<author><name sortKey="Auch, Af" uniqKey="Auch A">AF Auch</name>
</author>
<author><name sortKey="Qi, J" uniqKey="Qi J">J Qi</name>
</author>
<author><name sortKey="Schuster, Sc" uniqKey="Schuster S">SC Schuster</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brady, A" uniqKey="Brady A">A Brady</name>
</author>
<author><name sortKey="Salzberg, S" 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>
<double pmid="25879410"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative <italic>k</italic>
-mers</title>
<author><name sortKey="Ounit, Rachid" sort="Ounit, Rachid" uniqKey="Ounit R" first="Rachid" last="Ounit">Rachid Ounit</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>
<author><name sortKey="Wanamaker, Steve" sort="Wanamaker, Steve" uniqKey="Wanamaker S" first="Steve" last="Wanamaker">Steve Wanamaker</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="Close, Timothy J" sort="Close, Timothy J" uniqKey="Close T" first="Timothy J" last="Close">Timothy J. 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>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">25879410</idno>
<idno type="pmc">4428112</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428112</idno>
<idno type="RBID">PMC:4428112</idno>
<idno type="doi">10.1186/s12864-015-1419-2</idno>
<date when="2015">2015</date>
<idno type="wicri:Area/Pmc/Corpus">000292</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000292</idno>
<idno type="wicri:Area/Pmc/Curation">000292</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000292</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000F01</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000F01</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative <italic>k</italic>
-mers</title>
<author><name sortKey="Ounit, Rachid" sort="Ounit, Rachid" uniqKey="Ounit R" first="Rachid" last="Ounit">Rachid Ounit</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>
<author><name sortKey="Wanamaker, Steve" sort="Wanamaker, Steve" uniqKey="Wanamaker S" first="Steve" last="Wanamaker">Steve Wanamaker</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="Close, Timothy J" sort="Close, Timothy J" uniqKey="Close T" first="Timothy J" last="Close">Timothy J. 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></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" uniqKey="Huttenhower C">C Huttenhower</name>
</author>
<author><name sortKey="Gevers, D" uniqKey="Gevers D">D Gevers</name>
</author>
<author><name sortKey="Knight, R" uniqKey="Knight R">R Knight</name>
</author>
<author><name sortKey="Abubucker, S" uniqKey="Abubucker S">S Abubucker</name>
</author>
<author><name sortKey="Badger, Jh" uniqKey="Badger J">JH Badger</name>
</author>
<author><name sortKey="Chinwalla, At" uniqKey="Chinwalla A">AT Chinwalla</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Huson, Dh" uniqKey="Huson D">DH Huson</name>
</author>
<author><name sortKey="Auch, Af" uniqKey="Auch A">AF Auch</name>
</author>
<author><name sortKey="Qi, J" uniqKey="Qi J">J Qi</name>
</author>
<author><name sortKey="Schuster, Sc" uniqKey="Schuster S">SC Schuster</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brady, A" uniqKey="Brady A">A Brady</name>
</author>
<author><name sortKey="Salzberg, S" 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>
</pmc>
<pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.</title>
<author><name sortKey="Ounit, Rachid" sort="Ounit, Rachid" uniqKey="Ounit R" first="Rachid" last="Ounit">Rachid Ounit</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science & Engineering, University of California, 900 University Avenue, CA, 92521, Riverside, USA. rouni001@cs.ucr.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science & Engineering, University of California, 900 University Avenue, CA, 92521, Riverside</wicri:regionArea>
<wicri:noRegion>Riverside</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Wanamaker, Steve" sort="Wanamaker, Steve" uniqKey="Wanamaker S" first="Steve" last="Wanamaker">Steve Wanamaker</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Plant & Botanic Sciences, University of California, 900 University Avenue, CA, 92521, Riverside, USA. steve.wanamaker@ucr.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Plant & Botanic Sciences, University of California, 900 University Avenue, CA, 92521, Riverside</wicri:regionArea>
<wicri:noRegion>Riverside</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Close, Timothy J" sort="Close, Timothy J" uniqKey="Close T" first="Timothy J" last="Close">Timothy J. Close</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Plant & Botanic Sciences, University of California, 900 University Avenue, CA, 92521, Riverside, USA. timothy.close@ucr.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Plant & Botanic Sciences, University of California, 900 University Avenue, CA, 92521, Riverside</wicri:regionArea>
<wicri:noRegion>Riverside</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Lonardi, Stefano" sort="Lonardi, Stefano" uniqKey="Lonardi S" first="Stefano" last="Lonardi">Stefano Lonardi</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science & Engineering, University of California, 900 University Avenue, CA, 92521, Riverside, USA. stelo@cs.ucr.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science & Engineering, University of California, 900 University Avenue, CA, 92521, Riverside</wicri:regionArea>
<wicri:noRegion>Riverside</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2015">2015</date>
<idno type="RBID">pubmed:25879410</idno>
<idno type="pmid">25879410</idno>
<idno type="doi">10.1186/s12864-015-1419-2</idno>
<idno type="wicri:Area/PubMed/Corpus">001644</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001644</idno>
<idno type="wicri:Area/PubMed/Curation">001644</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001644</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001619</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001619</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.</title>
<author><name sortKey="Ounit, Rachid" sort="Ounit, Rachid" uniqKey="Ounit R" first="Rachid" last="Ounit">Rachid Ounit</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science & Engineering, University of California, 900 University Avenue, CA, 92521, Riverside, USA. rouni001@cs.ucr.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science & Engineering, University of California, 900 University Avenue, CA, 92521, Riverside</wicri:regionArea>
<wicri:noRegion>Riverside</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Wanamaker, Steve" sort="Wanamaker, Steve" uniqKey="Wanamaker S" first="Steve" last="Wanamaker">Steve Wanamaker</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Plant & Botanic Sciences, University of California, 900 University Avenue, CA, 92521, Riverside, USA. steve.wanamaker@ucr.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Plant & Botanic Sciences, University of California, 900 University Avenue, CA, 92521, Riverside</wicri:regionArea>
<wicri:noRegion>Riverside</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Close, Timothy J" sort="Close, Timothy J" uniqKey="Close T" first="Timothy J" last="Close">Timothy J. Close</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Plant & Botanic Sciences, University of California, 900 University Avenue, CA, 92521, Riverside, USA. timothy.close@ucr.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Plant & Botanic Sciences, University of California, 900 University Avenue, CA, 92521, Riverside</wicri:regionArea>
<wicri:noRegion>Riverside</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Lonardi, Stefano" sort="Lonardi, Stefano" uniqKey="Lonardi S" first="Stefano" last="Lonardi">Stefano Lonardi</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science & Engineering, University of California, 900 University Avenue, CA, 92521, Riverside, USA. stelo@cs.ucr.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science & Engineering, University of California, 900 University Avenue, CA, 92521, Riverside</wicri:regionArea>
<wicri:noRegion>Riverside</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2015" type="published">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">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.</div>
</front>
</TEI>
</pubmed>
</double>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001097 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd -nk 001097 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Ncbi |étape= Merge |type= RBID |clé= PMC:4428112 |texte= CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:25879410" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
This area was generated with Dilib version V0.6.33. |