CoMeta: Classification of Metagenomes Using k-mers
Identifieur interne : 000E92 ( Pmc/Checkpoint ); précédent : 000E91; suivant : 000E93CoMeta: Classification of Metagenomes Using k-mers
Auteurs : Jolanta Kawulok ; Sebastian DeorowiczSource :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions. An important element of extracting the knowledge of the sample composition is to compare the extracted fragments of DNA with sequences derived from known organisms. In the presented paper, we introduce an algorithm called CoMeta (
Url:
DOI: 10.1371/journal.pone.0121453
PubMed: 25884504
PubMed Central: 4401624
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">CoMeta: Classification of Metagenomes Using <italic>k</italic>-mers</title><author><name sortKey="Kawulok, Jolanta" sort="Kawulok, Jolanta" uniqKey="Kawulok J" first="Jolanta" last="Kawulok">Jolanta Kawulok</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25884504</idno><idno type="pmc">4401624</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401624</idno><idno type="RBID">PMC:4401624</idno><idno type="doi">10.1371/journal.pone.0121453</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">001006</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001006</idno><idno type="wicri:Area/Pmc/Curation">001006</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001006</idno><idno type="wicri:Area/Pmc/Checkpoint">000E92</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000E92</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">CoMeta: Classification of Metagenomes Using <italic>k</italic>-mers</title><author><name sortKey="Kawulok, Jolanta" sort="Kawulok, Jolanta" uniqKey="Kawulok J" first="Jolanta" last="Kawulok">Jolanta Kawulok</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions. An important element of extracting the knowledge of the sample composition is to compare the extracted fragments of DNA with sequences derived from known organisms. In the presented paper, we introduce an algorithm called CoMeta (<underline>C</underline>lassification <underline>o</underline>f <underline>meta</underline>genomes), which assigns a query read (a DNA fragment) into one of the groups previously prepared by the user. Typically, this is one of the taxonomic rank (e.g., phylum, genus), however prepared groups may contain sequences having various functions. In CoMeta, we used the exact method for read classification using short subsequences (<italic>k</italic>-mers) and fast program for indexing large set of <italic>k</italic>-mers. In contrast to the most popular methods based on BLAST, where the query is compared with each reference sequence, we begin the classification from the top of the taxonomy tree to reduce the number of comparisons. The presented experimental study confirms that CoMeta outperforms other programs used in this context. CoMeta is available at <ext-link ext-link-type="uri" xlink:href="https://github.com/jkawulok/cometa">https://github.com/jkawulok/cometa</ext-link> under a free GNU GPL 2 license.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Handelsman, J" uniqKey="Handelsman J">J Handelsman</name></author><author><name sortKey="Rondon, Mr" uniqKey="Rondon M">MR Rondon</name></author><author><name sortKey="Brady, Sf" uniqKey="Brady S">SF Brady</name></author><author><name sortKey="Clardy, J" uniqKey="Clardy J">J Clardy</name></author><author><name sortKey="Goodman, Rm" uniqKey="Goodman R">RM Goodman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pace, Nr" uniqKey="Pace N">NR Pace</name></author><author><name sortKey="Stahl, Da" uniqKey="Stahl D">DA Stahl</name></author><author><name sortKey="Olsen, Gj" uniqKey="Olsen G">GJ Olsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Handelsman, J" uniqKey="Handelsman J">J Handelsman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simon, C" uniqKey="Simon C">C Simon</name></author><author><name sortKey="Daniel, R" uniqKey="Daniel R">R Daniel</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Rousk, J" uniqKey="Rousk J">J Rousk</name></author><author><name sortKey="Baath, E" uniqKey="Baath E">E Baath</name></author><author><name sortKey="Brookes, Pc" uniqKey="Brookes P">PC Brookes</name></author><author><name sortKey="Lauber, Cl" uniqKey="Lauber C">CL Lauber</name></author><author><name sortKey="Lozupone, C" uniqKey="Lozupone C">C Lozupone</name></author><author><name sortKey="Caporaso, Jg" uniqKey="Caporaso J">JG Caporaso</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fierer, N" uniqKey="Fierer N">N Fierer</name></author><author><name sortKey="Leff, J" uniqKey="Leff J">J Leff</name></author><author><name sortKey="Adams, B" uniqKey="Adams B">B Adams</name></author><author><name sortKey="Nielsen, U" uniqKey="Nielsen U">U Nielsen</name></author><author><name sortKey="Bates, S" uniqKey="Bates S">S Bates</name></author><author><name sortKey="Lauber, C" uniqKey="Lauber C">C Lauber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Abbai, N" uniqKey="Abbai N">N Abbai</name></author><author><name sortKey="Govender, A" uniqKey="Govender A">A Govender</name></author><author><name sortKey="Shaik, R" uniqKey="Shaik R">R Shaik</name></author><author><name sortKey="Pillay, B" uniqKey="Pillay B">B Pillay</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kennedy, J" uniqKey="Kennedy J">J Kennedy</name></author><author><name sortKey="O Eary, Nd" uniqKey="O Eary N">ND O’Leary</name></author><author><name sortKey="Kiran, Gs" uniqKey="Kiran G">GS Kiran</name></author><author><name sortKey="Morrissey, Jp" uniqKey="Morrissey J">JP Morrissey</name></author><author><name sortKey="O Ara, F" uniqKey="O Ara F">F O’Gara</name></author><author><name sortKey="Selvin, J" uniqKey="Selvin J">J Selvin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gilbert, J" uniqKey="Gilbert J">J Gilbert</name></author><author><name sortKey="Field, D" uniqKey="Field D">D Field</name></author><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y Huang</name></author><author><name sortKey="Edwards, R" uniqKey="Edwards R">R Edwards</name></author><author><name sortKey="Li, W" uniqKey="Li W">W Li</name></author><author><name sortKey="Gilna, P" uniqKey="Gilna P">P Gilna</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yergeau, E" uniqKey="Yergeau E">E Yergeau</name></author><author><name sortKey="Lawrence, Jr" uniqKey="Lawrence J">JR Lawrence</name></author><author><name sortKey="Waiser, Mj" uniqKey="Waiser M">MJ Waiser</name></author><author><name sortKey="Korber, Dr" uniqKey="Korber D">DR Korber</name></author><author><name sortKey="Greer, Cw" uniqKey="Greer C">CW Greer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rhee, Jk" uniqKey="Rhee J">JK Rhee</name></author><author><name sortKey="Ahn, Dg" uniqKey="Ahn D">DG Ahn</name></author><author><name sortKey="Kim, Yg" uniqKey="Kim Y">YG Kim</name></author><author><name sortKey="Oh, Jw" uniqKey="Oh J">JW Oh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simon, C" uniqKey="Simon C">C Simon</name></author><author><name sortKey="Wiezer, A" uniqKey="Wiezer A">A Wiezer</name></author><author><name sortKey="Strittmatter, Aw" uniqKey="Strittmatter A">AW Strittmatter</name></author><author><name sortKey="Daniel, R" uniqKey="Daniel R">R Daniel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Heath, C" uniqKey="Heath C">C Heath</name></author><author><name sortKey="Hu, Xpp" uniqKey="Hu X">XPP Hu</name></author><author><name sortKey="Cary, Sc" uniqKey="Cary S">SC Cary</name></author><author><name sortKey="Cowan, D" uniqKey="Cowan D">D Cowan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nguyen, Nh" uniqKey="Nguyen N">NH Nguyen</name></author><author><name sortKey="Maruset, L" uniqKey="Maruset L">L Maruset</name></author><author><name sortKey="Uengwetwanit, T" uniqKey="Uengwetwanit T">T Uengwetwanit</name></author><author><name sortKey="Mhuantong, W" uniqKey="Mhuantong W">W Mhuantong</name></author><author><name sortKey="Harnpicharnchai, P" uniqKey="Harnpicharnchai P">P Harnpicharnchai</name></author><author><name sortKey="Champreda, V" uniqKey="Champreda V">V Champreda</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hess, M" uniqKey="Hess M">M Hess</name></author><author><name sortKey="Sczyrba, A" uniqKey="Sczyrba A">A Sczyrba</name></author><author><name sortKey="Egan, R" uniqKey="Egan R">R Egan</name></author><author><name sortKey="Kim, T" uniqKey="Kim T">T Kim</name></author><author><name sortKey="Chokhawala, H" uniqKey="Chokhawala H">H Chokhawala</name></author><author><name sortKey="Schroth, G" uniqKey="Schroth G">G Schroth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qin, J" uniqKey="Qin J">J Qin</name></author><author><name sortKey="Li, R" uniqKey="Li R">R Li</name></author><author><name sortKey="Raes, J" uniqKey="Raes J">J Raes</name></author><author><name sortKey="Arumugam, M" uniqKey="Arumugam M">M Arumugam</name></author><author><name sortKey="Burgdorf, K" uniqKey="Burgdorf K">K Burgdorf</name></author><author><name sortKey="Manichanh, C" uniqKey="Manichanh C">C Manichanh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kuczynski, J" uniqKey="Kuczynski J">J Kuczynski</name></author><author><name sortKey="Lauber, Cl" uniqKey="Lauber C">CL Lauber</name></author><author><name sortKey="Walters, Wa" uniqKey="Walters W">WA Walters</name></author><author><name sortKey="Parfrey, Lw" uniqKey="Parfrey L">LW Parfrey</name></author><author><name sortKey="Clemente, Jc" uniqKey="Clemente J">JC Clemente</name></author><author><name sortKey="Gevers, D" uniqKey="Gevers D">D Gevers</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bruls, T" uniqKey="Bruls T">T Bruls</name></author><author><name sortKey="Weissenbach, J" uniqKey="Weissenbach J">J Weissenbach</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peterson, J" uniqKey="Peterson J">J Peterson</name></author><author><name sortKey="Garges, S" uniqKey="Garges S">S Garges</name></author><author><name sortKey="Giovanni, M" uniqKey="Giovanni M">M Giovanni</name></author><author><name sortKey="Mcinnes, P" uniqKey="Mcinnes P">P McInnes</name></author><author><name sortKey="Wang, L" uniqKey="Wang L">L Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thomas, T" uniqKey="Thomas T">T Thomas</name></author><author><name sortKey="Gilbert, J" uniqKey="Gilbert J">J Gilbert</name></author><author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kunin, V" uniqKey="Kunin V">V Kunin</name></author><author><name sortKey="Copeland, A" uniqKey="Copeland A">A Copeland</name></author><author><name sortKey="Lapidus, A" uniqKey="Lapidus A">A Lapidus</name></author><author><name sortKey="Mavromatis, K" uniqKey="Mavromatis K">K Mavromatis</name></author><author><name sortKey="Hugenholtz, P" uniqKey="Hugenholtz P">P Hugenholtz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanger, F" uniqKey="Sanger F">F Sanger</name></author><author><name sortKey="Nicklen, S" uniqKey="Nicklen S">S Nicklen</name></author><author><name sortKey="Coulson, Ar" uniqKey="Coulson A">AR Coulson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Metzker, Ml" uniqKey="Metzker M">ML Metzker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nalbantoglu, U" uniqKey="Nalbantoglu U">U Nalbantoglu</name></author><author><name sortKey="Cakar, A" uniqKey="Cakar A">A Cakar</name></author><author><name sortKey="Dogan, H" uniqKey="Dogan H">H Dogan</name></author><author><name sortKey="Abaci, N" uniqKey="Abaci N">N Abaci</name></author><author><name sortKey="Ustek, D" uniqKey="Ustek D">D Ustek</name></author><author><name sortKey="Sayood, K" uniqKey="Sayood K">K Sayood</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Z" uniqKey="Wang Z">Z Wang</name></author><author><name sortKey="Yang, J" uniqKey="Yang J">J Yang</name></author><author><name sortKey="Zhou, J" uniqKey="Zhou J">J Zhou</name></author><author><name sortKey="Zhang, C" uniqKey="Zhang C">C Zhang</name></author><author><name sortKey="Su, X" uniqKey="Su X">X Su</name></author><author><name sortKey="Li, T" uniqKey="Li T">T Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shafquat, A" uniqKey="Shafquat A">A Shafquat</name></author><author><name sortKey="Joice, R" uniqKey="Joice R">R Joice</name></author><author><name sortKey="Simmons, Sl" uniqKey="Simmons S">SL Simmons</name></author><author><name sortKey="Huttenhower, C" uniqKey="Huttenhower C">C Huttenhower</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hauser, Pm" uniqKey="Hauser P">PM Hauser</name></author><author><name sortKey="Bernard, T" uniqKey="Bernard T">T Bernard</name></author><author><name sortKey="Greub, G" uniqKey="Greub G">G Greub</name></author><author><name sortKey="Jaton, K" uniqKey="Jaton K">K Jaton</name></author><author><name sortKey="Pagni, M" uniqKey="Pagni M">M Pagni</name></author><author><name sortKey="Hafen, Gm" uniqKey="Hafen G">GM Hafen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Benson, Da" uniqKey="Benson D">DA Benson</name></author><author><name sortKey="Cavanaugh, M" uniqKey="Cavanaugh M">M Cavanaugh</name></author><author><name sortKey="Clark, K" uniqKey="Clark K">K Clark</name></author><author><name sortKey="Karsch Mizrachi, I" uniqKey="Karsch Mizrachi I">I Karsch-Mizrachi</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author><author><name sortKey="Ostell, J" uniqKey="Ostell J">J Ostell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fierer, N" uniqKey="Fierer N">N Fierer</name></author><author><name sortKey="Breitbart, M" uniqKey="Breitbart M">M Breitbart</name></author><author><name sortKey="Nulton, J" uniqKey="Nulton J">J Nulton</name></author><author><name sortKey="Salamon, P" uniqKey="Salamon P">P Salamon</name></author><author><name sortKey="Lozupone, C" uniqKey="Lozupone C">C Lozupone</name></author><author><name sortKey="Jones, R" uniqKey="Jones R">R Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simister, R" uniqKey="Simister R">R Simister</name></author><author><name sortKey="Taylor, Mw" uniqKey="Taylor M">MW Taylor</name></author><author><name sortKey="Tsai, P" uniqKey="Tsai P">P Tsai</name></author><author><name sortKey="Fan, L" uniqKey="Fan L">L Fan</name></author><author><name sortKey="Bruxner, Tj" uniqKey="Bruxner T">TJ Bruxner</name></author><author><name sortKey="Crowe, Ml" uniqKey="Crowe M">ML Crowe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krogius Kurikka, L" uniqKey="Krogius Kurikka L">L Krogius-Kurikka</name></author><author><name sortKey="Kassinen, A" uniqKey="Kassinen A">A Kassinen</name></author><author><name sortKey="Paulin, L" uniqKey="Paulin L">L Paulin</name></author><author><name sortKey="Corander, J" uniqKey="Corander J">J Corander</name></author><author><name sortKey="Makivuokko, H" uniqKey="Makivuokko H">H Makivuokko</name></author><author><name sortKey="Tuimala, J" uniqKey="Tuimala J">J Tuimala</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Mclenachan, Pa" uniqKey="Mclenachan P">PA McLenachan</name></author><author><name sortKey="Biggs, Pj" uniqKey="Biggs P">PJ Biggs</name></author><author><name sortKey="Winder, Lh" uniqKey="Winder L">LH Winder</name></author><author><name sortKey="Schoenfeld, Bik" uniqKey="Schoenfeld B">BIK Schoenfeld</name></author><author><name sortKey="Narayan, Vv" uniqKey="Narayan V">VV Narayan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brady, A" uniqKey="Brady A">A Brady</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Diaz, Nn" uniqKey="Diaz N">NN Diaz</name></author><author><name sortKey="Krause, L" uniqKey="Krause L">L Krause</name></author><author><name sortKey="Goesmann, A" uniqKey="Goesmann A">A Goesmann</name></author><author><name sortKey="Niehaus, K" uniqKey="Niehaus K">K Niehaus</name></author><author><name sortKey="Nattkemper, Tw" uniqKey="Nattkemper T">TW Nattkemper</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="Cui, H" uniqKey="Cui H">H Cui</name></author><author><name sortKey="Zhang, X" uniqKey="Zhang X">X Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kawulok, M" uniqKey="Kawulok M">M Kawulok</name></author><author><name sortKey="Nalepa, J" uniqKey="Nalepa J">J Nalepa</name></author><author><name sortKey="Gimel Arb, G" uniqKey="Gimel Arb G">G Gimel’farb</name></author><author><name sortKey="Hancock, E" uniqKey="Hancock E">E Hancock</name></author><author><name sortKey="Imiya, A" uniqKey="Imiya A">A Imiya</name></author><author><name sortKey="Kuijper, A" uniqKey="Kuijper A">A Kuijper</name></author><author><name sortKey="Kudo, M" uniqKey="Kudo M">M Kudo</name></author><author><name sortKey="Omachi, S" uniqKey="Omachi S">S Omachi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cyran, Ka" uniqKey="Cyran K">KA Cyran</name></author><author><name sortKey="Kawulok, J" uniqKey="Kawulok J">J Kawulok</name></author><author><name sortKey="Kawulok, M" uniqKey="Kawulok M">M Kawulok</name></author><author><name sortKey="Stawarz, M" uniqKey="Stawarz M">M Stawarz</name></author><author><name sortKey="Michalak, M" uniqKey="Michalak M">M Michalak</name></author><author><name sortKey="Pietrowska, M" uniqKey="Pietrowska M">M Pietrowska</name></author><author><name sortKey="Ramanna, S" uniqKey="Ramanna S">S Ramanna</name></author><author><name sortKey="Jain, Lc" uniqKey="Jain L">LC Jain</name></author><author><name sortKey="Howlett, Rj" uniqKey="Howlett R">RJ Howlett</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, D" uniqKey="Wang D">D Wang</name></author><author><name sortKey="Shi, L" uniqKey="Shi L">L Shi</name></author></analytic></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="Gori, F" uniqKey="Gori F">F Gori</name></author><author><name sortKey="Folino, G" uniqKey="Folino G">G Folino</name></author><author><name sortKey="Jetten, Msm" uniqKey="Jetten M">MSM Jetten</name></author><author><name sortKey="Marchiori, E" uniqKey="Marchiori E">E Marchiori</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Monzoorul Haque, M" uniqKey="Monzoorul Haque M">M Monzoorul Haque</name></author><author><name sortKey="Ghosh, Ts" uniqKey="Ghosh T">TS Ghosh</name></author><author><name sortKey="Komanduri, D" uniqKey="Komanduri D">D Komanduri</name></author><author><name sortKey="Mande, Ss" uniqKey="Mande S">SS Mande</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gerlach, W" uniqKey="Gerlach W">W Gerlach</name></author><author><name sortKey="Stoye, J" uniqKey="Stoye J">J Stoye</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name></author><author><name sortKey="Paarmann, D" uniqKey="Paarmann D">D Paarmann</name></author><author><name sortKey="D Ouza, M" uniqKey="D Ouza M">M D’Souza</name></author><author><name sortKey="Olson, R" uniqKey="Olson R">R Olson</name></author><author><name sortKey="Glass, E" uniqKey="Glass E">E Glass</name></author><author><name sortKey="Kubal, M" uniqKey="Kubal M">M Kubal</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Schreiber, F" uniqKey="Schreiber F">F Schreiber</name></author><author><name sortKey="Gumrich, P" uniqKey="Gumrich P">P Gumrich</name></author><author><name sortKey="Daniel, R" uniqKey="Daniel R">R Daniel</name></author><author><name sortKey="Meinicke, P" uniqKey="Meinicke P">P Meinicke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stranneheim, H" uniqKey="Stranneheim H">H Stranneheim</name></author><author><name sortKey="Kaller, M" uniqKey="Kaller M">M Kaller</name></author><author><name sortKey="Allander, T" uniqKey="Allander T">T Allander</name></author><author><name sortKey="Andersson, B" uniqKey="Andersson B">B Andersson</name></author><author><name sortKey="Arvestad, L" uniqKey="Arvestad L">L Arvestad</name></author><author><name sortKey="Lundeberg, J" uniqKey="Lundeberg J">J Lundeberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ames, S" uniqKey="Ames S">S 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, De" uniqKey="Wood D">DE Wood</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Roberts, M" uniqKey="Roberts M">M Roberts</name></author><author><name sortKey="Hayes, W" uniqKey="Hayes W">W Hayes</name></author><author><name sortKey="Hunt, Br" uniqKey="Hunt B">BR Hunt</name></author><author><name sortKey="Mount, Sm" uniqKey="Mount S">SM Mount</name></author><author><name sortKey="Yorke, Ja" uniqKey="Yorke J">JA Yorke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Deorowicz, S" uniqKey="Deorowicz S">S Deorowicz</name></author><author><name sortKey="Kokot, M" uniqKey="Kokot M">M Kokot</name></author><author><name sortKey="Grabowski, S" uniqKey="Grabowski S">S Grabowski</name></author><author><name sortKey="Debudaj Grabysz, A" uniqKey="Debudaj Grabysz A">A Debudaj-Grabysz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Movahedi, Ns" uniqKey="Movahedi N">NS Movahedi</name></author><author><name sortKey="Forouzmand, E" uniqKey="Forouzmand E">E Forouzmand</name></author><author><name sortKey="Chitsaz, H" uniqKey="Chitsaz H">H Chitsaz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Deorowicz, S" uniqKey="Deorowicz S">S Deorowicz</name></author><author><name sortKey="Debudaj Grabysz, A" uniqKey="Debudaj Grabysz A">A Debudaj-Grabysz</name></author><author><name sortKey="Grabowski, S" uniqKey="Grabowski S">S Grabowski</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="Kawulok, J" uniqKey="Kawulok J">J Kawulok</name></author><author><name sortKey="Deorowicz, S" uniqKey="Deorowicz S">S Deorowicz</name></author><author><name sortKey="Kozielski, S" uniqKey="Kozielski S">S Kozielski</name></author><author><name sortKey="Mrozek, D" uniqKey="Mrozek D">D Mrozek</name></author><author><name sortKey="Kasprowski, P" uniqKey="Kasprowski P">P Kasprowski</name></author><author><name sortKey="Maysiak Mrozek, B" uniqKey="Maysiak Mrozek B">B Maysiak-Mrozek</name></author><author><name sortKey="Kostrzewa, D" uniqKey="Kostrzewa D">D Kostrzewa</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25884504</article-id><article-id pub-id-type="pmc">4401624</article-id><article-id pub-id-type="publisher-id">PONE-D-14-28208</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0121453</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>CoMeta: Classification of Metagenomes Using <italic>k</italic>-mers</article-title><alt-title alt-title-type="running-head">CoMeta: Classification of Metagenomes Using <italic>k</italic>-mers</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Kawulok</surname><given-names>Jolanta</given-names></name><xref ref-type="corresp" rid="cor001">*</xref><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Deorowicz</surname><given-names>Sebastian</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib></contrib-group><aff id="aff001"><addr-line>Institute of Informatics, Silesian University of Technology, Gliwice, Poland</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Golden</surname><given-names>Aaron Alain-Jon</given-names></name><role>Academic Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Albert Einstein College of Medicine, UNITED STATES</addr-line></aff><author-notes><fn fn-type="COI-statement" id="coi001"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: JK SD. Performed the experiments: JK. Analyzed the data: JK. Contributed reagents/materials/analysis tools: JK SD. Wrote the paper: JK SD. Designed the software: JK SD.</p></fn><corresp id="cor001">* E-mail: <email>jolanta.kawulok@polsl.pl</email></corresp></author-notes><pub-date pub-type="collection"><year>2015</year></pub-date><pub-date pub-type="epub"><day>17</day><month>4</month><year>2015</year></pub-date><volume>10</volume><issue>4</issue><elocation-id>e0121453</elocation-id><history><date date-type="received"><day>24</day><month>6</month><year>2014</year></date><date date-type="accepted"><day>15</day><month>2</month><year>2015</year></date></history><permissions><copyright-statement>© 2015 Kawulok, Deorowicz</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Kawulok, Deorowicz</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0121453.pdf"></self-uri><abstract><p>Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions. An important element of extracting the knowledge of the sample composition is to compare the extracted fragments of DNA with sequences derived from known organisms. In the presented paper, we introduce an algorithm called CoMeta (<underline>C</underline>lassification <underline>o</underline>f <underline>meta</underline>genomes), which assigns a query read (a DNA fragment) into one of the groups previously prepared by the user. Typically, this is one of the taxonomic rank (e.g., phylum, genus), however prepared groups may contain sequences having various functions. In CoMeta, we used the exact method for read classification using short subsequences (<italic>k</italic>-mers) and fast program for indexing large set of <italic>k</italic>-mers. In contrast to the most popular methods based on BLAST, where the query is compared with each reference sequence, we begin the classification from the top of the taxonomy tree to reduce the number of comparisons. The presented experimental study confirms that CoMeta outperforms other programs used in this context. CoMeta is available at <ext-link ext-link-type="uri" xlink:href="https://github.com/jkawulok/cometa">https://github.com/jkawulok/cometa</ext-link> under a free GNU GPL 2 license.</p></abstract><funding-group><funding-statement>This work was supported by the Polish National Science Centre under the project DEC-2012/05/B/ST6/03148 and the European Union from the European Social Fund (grant agreement number: UDA-POKL.04.01.01-00-106/09). The work was performed using the infrastructure supported by POIG.02.03.01-24-099/13 grant: "GeCONiI---Upper Silesian Center for Computational Science and Engineering". This research was supported in part by PL-Grid Infrastructure. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><fig-count count="5"></fig-count><table-count count="6"></table-count><page-count count="23"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>The package and documentation of the program are freely available at <ext-link ext-link-type="uri" xlink:href="https://github.com/jkawulok/cometa">https://github.com/jkawulok/cometa</ext-link>, all the data used in this paper are available at <ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.7910/DVN/29265">http://dx.doi.org/10.7910/DVN/29265</ext-link>.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>The package and documentation of the program are freely available at <ext-link ext-link-type="uri" xlink:href="https://github.com/jkawulok/cometa">https://github.com/jkawulok/cometa</ext-link>, all the data used in this paper are available at <ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.7910/DVN/29265">http://dx.doi.org/10.7910/DVN/29265</ext-link>.</p></notes></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name><name sortKey="Kawulok, Jolanta" sort="Kawulok, Jolanta" uniqKey="Kawulok J" first="Jolanta" last="Kawulok">Jolanta Kawulok</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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