CoMeta: Classification of Metagenomes Using k-mers
Identifieur interne : 001860 ( Main/Exploration ); précédent : 001859; suivant : 001861CoMeta: Classification of Metagenomes Using k-mers
Auteurs : Jolanta Kawulok ; Sebastian DeorowiczSource :
- PLoS ONE [ 1932-6203 ] ; 2015.
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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
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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><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:25884504</idno><idno type="wicri:Area/PubMed/Corpus">001643</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001643</idno><idno type="wicri:Area/PubMed/Curation">001643</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001643</idno><idno type="wicri:Area/PubMed/Checkpoint">001607</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001607</idno><idno type="wicri:Area/Ncbi/Merge">001098</idno><idno type="wicri:Area/Ncbi/Curation">001098</idno><idno type="wicri:Area/Ncbi/Checkpoint">001098</idno><idno type="wicri:Area/Main/Merge">001865</idno><idno type="wicri:Area/Main/Curation">001860</idno><idno type="wicri:Area/Main/Exploration">001860</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><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Databases, Genetic</term><term>Internet</term><term>Metagenomics (methods)</term><term>Sequence Analysis, DNA</term><term>User-Computer Interface</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Bases de données génétiques</term><term>Interface utilisateur</term><term>Internet</term><term>Métagénomique ()</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Databases, Genetic</term><term>Internet</term><term>Sequence Analysis, DNA</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Bases de données génétiques</term><term>Interface utilisateur</term><term>Internet</term><term>Métagénomique</term></keywords></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 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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><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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