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CoMeta: Classification of Metagenomes Using k-mers

Identifieur interne : 000E92 ( Pmc/Checkpoint ); précédent : 000E91; suivant : 000E93

CoMeta: Classification of Metagenomes Using k-mers

Auteurs : Jolanta Kawulok ; Sebastian Deorowicz

Source :

RBID : PMC:4401624

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 (Classification of metagenomes), 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 (k-mers) and fast program for indexing large set of k-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 https://github.com/jkawulok/cometa under a free GNU GPL 2 license.


Url:
DOI: 10.1371/journal.pone.0121453
PubMed: 25884504
PubMed Central: 4401624


Affiliations:


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PMC:4401624

Le document en format XML

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</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>

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