Real Time Metagenomics: Using k-mers to annotate metagenomes
Identifieur interne : 001284 ( Pmc/Checkpoint ); précédent : 001283; suivant : 001285Real Time Metagenomics: Using k-mers to annotate metagenomes
Auteurs : Robert A. Edwards [États-Unis] ; Robert Olson [États-Unis] ; Terry Disz [États-Unis] ; Gordon D. Pusch [États-Unis] ; Veronika Vonstein [États-Unis] ; Rick Stevens [États-Unis] ; Ross Overbeek [États-Unis]Source :
- Bioinformatics [ 1367-4803 ] ; 2012.
Abstract
Url:
DOI: 10.1093/bioinformatics/bts599
PubMed: 23047562
PubMed Central: 3519453
Affiliations:
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PMC:3519453Le document en format XML
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-mers to annotate metagenomes</title>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Real Time Metagenomics: Using <italic>k</italic>
-mers to annotate metagenomes</title>
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<author><name sortKey="Vonstein, Veronika" sort="Vonstein, Veronika" uniqKey="Vonstein V" first="Veronika" last="Vonstein">Veronika Vonstein</name>
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<settlement type="city">Chicago</settlement>
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</affiliation>
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<author><name sortKey="Overbeek, Ross" sort="Overbeek, Ross" uniqKey="Overbeek R" first="Ross" last="Overbeek">Ross Overbeek</name>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527</wicri:regionArea>
<placeName><region type="state">Illinois</region>
</placeName>
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<idno type="ISSN">1367-4803</idno>
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<front><div type="abstract" xml:lang="en"><p><bold>Summary:</bold>
Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique <italic>k</italic>
-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that <italic>k-</italic>
mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.</p>
<p><bold>Availability and implementation:</bold>
This open-source application was implemented in Perl and can be accessed via a user-friendly website at <ext-link ext-link-type="uri" xlink:href="http://edwards.sdsu.edu/rtmg">http://edwards.sdsu.edu/rtmg</ext-link>
. In addition, code to access the annotation servers is available for download from <ext-link ext-link-type="uri" xlink:href="http://www.theseed.org/">http://www.theseed.org/</ext-link>
. FIGfams and <italic>k</italic>
-mers are available for download from <ext-link ext-link-type="ftp" xlink:href="ftp://ftp.theseed.org/FIGfams/">ftp://ftp.theseed.org/FIGfams/</ext-link>
.</p>
<p><bold>Contact:</bold>
<email>redwards@mail.sdsu.edu</email>
</p>
<p><bold>Supplementary information:</bold>
<ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/bts599/DC1">Supplementary data</ext-link>
are available at <italic>Bioinformatics</italic>
online.</p>
</div>
</front>
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</author>
</analytic>
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<biblStruct><analytic><author><name sortKey="Dinsdale, E A" uniqKey="Dinsdale E">E.A. Dinsdale</name>
</author>
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<biblStruct><analytic><author><name sortKey="Meyer, F" uniqKey="Meyer F">F. Meyer</name>
</author>
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<biblStruct><analytic><author><name sortKey="Meyer, F" uniqKey="Meyer F">F. Meyer</name>
</author>
</analytic>
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<biblStruct><analytic><author><name sortKey="Overbeek, R" uniqKey="Overbeek R">R. Overbeek</name>
</author>
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<biblStruct><analytic><author><name sortKey="Wilkening, J" uniqKey="Wilkening J">J. Wilkening</name>
</author>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">Bioinformatics</journal-id>
<journal-id journal-id-type="publisher-id">bioinformatics</journal-id>
<journal-id journal-id-type="hwp">bioinfo</journal-id>
<journal-title-group><journal-title>Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="ppub">1367-4803</issn>
<issn pub-type="epub">1367-4811</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23047562</article-id>
<article-id pub-id-type="pmc">3519453</article-id>
<article-id pub-id-type="doi">10.1093/bioinformatics/bts599</article-id>
<article-id pub-id-type="publisher-id">bts599</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Applications Note</subject>
<subj-group><subject>Genome Analysis</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Real Time Metagenomics: Using <italic>k</italic>
-mers to annotate metagenomes</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Edwards</surname>
<given-names>Robert A.</given-names>
</name>
<xref ref-type="aff" rid="bts599-AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="bts599-AFF1"><sup>2</sup>
</xref>
<xref ref-type="aff" rid="bts599-AFF1"><sup>3</sup>
</xref>
<xref ref-type="corresp" rid="bts599-COR1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Olson</surname>
<given-names>Robert</given-names>
</name>
<xref ref-type="aff" rid="bts599-AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="bts599-AFF1"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Disz</surname>
<given-names>Terry</given-names>
</name>
<xref ref-type="aff" rid="bts599-AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="bts599-AFF1"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pusch</surname>
<given-names>Gordon D.</given-names>
</name>
<xref ref-type="aff" rid="bts599-AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="bts599-AFF1"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Vonstein</surname>
<given-names>Veronika</given-names>
</name>
<xref ref-type="aff" rid="bts599-AFF1"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Stevens</surname>
<given-names>Rick</given-names>
</name>
<xref ref-type="aff" rid="bts599-AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="bts599-AFF1"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Overbeek</surname>
<given-names>Ross</given-names>
</name>
<xref ref-type="aff" rid="bts599-AFF1"><sup>5</sup>
</xref>
</contrib>
</contrib-group>
<aff id="bts599-AFF1"><sup>1</sup>
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA,<sup>2</sup>
Department of Biology,<sup>3</sup>
Department of Computer Science, San Diego State University, San Diego, CA 92182, USA,<sup>4</sup>
Computation Institute, University of Chicago, Chicago, IL 60637, USA and<sup>5</sup>
Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA</aff>
<author-notes><corresp id="bts599-COR1">*To whom correspondence should be addressed.</corresp>
<fn><p>Associate Editor: Michael Brudno</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>12</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>9</day>
<month>10</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>9</day>
<month>10</month>
<year>2012</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
. </pmc-comment>
<volume>28</volume>
<issue>24</issue>
<fpage>3316</fpage>
<lpage>3317</lpage>
<history><date date-type="received"><day>27</day>
<month>7</month>
<year>2012</year>
</date>
<date date-type="rev-recd"><day>7</day>
<month>9</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>28</day>
<month>9</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>© The Author 2012. Published by Oxford University Press.</copyright-statement>
<copyright-year>2012</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by/3.0"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link>
), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract><p><bold>Summary:</bold>
Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique <italic>k</italic>
-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that <italic>k-</italic>
mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.</p>
<p><bold>Availability and implementation:</bold>
This open-source application was implemented in Perl and can be accessed via a user-friendly website at <ext-link ext-link-type="uri" xlink:href="http://edwards.sdsu.edu/rtmg">http://edwards.sdsu.edu/rtmg</ext-link>
. In addition, code to access the annotation servers is available for download from <ext-link ext-link-type="uri" xlink:href="http://www.theseed.org/">http://www.theseed.org/</ext-link>
. FIGfams and <italic>k</italic>
-mers are available for download from <ext-link ext-link-type="ftp" xlink:href="ftp://ftp.theseed.org/FIGfams/">ftp://ftp.theseed.org/FIGfams/</ext-link>
.</p>
<p><bold>Contact:</bold>
<email>redwards@mail.sdsu.edu</email>
</p>
<p><bold>Supplementary information:</bold>
<ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/bts599/DC1">Supplementary data</ext-link>
are available at <italic>Bioinformatics</italic>
online.</p>
</abstract>
<counts><page-count count="2"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Californie</li>
<li>Illinois</li>
</region>
<settlement><li>Chicago</li>
</settlement>
<orgName><li>Université de Chicago</li>
</orgName>
</list>
<tree><country name="États-Unis"><region name="Illinois"><name sortKey="Edwards, Robert A" sort="Edwards, Robert A" uniqKey="Edwards R" first="Robert A." last="Edwards">Robert A. Edwards</name>
</region>
<name sortKey="Disz, Terry" sort="Disz, Terry" uniqKey="Disz T" first="Terry" last="Disz">Terry Disz</name>
<name sortKey="Disz, Terry" sort="Disz, Terry" uniqKey="Disz T" first="Terry" last="Disz">Terry Disz</name>
<name sortKey="Edwards, Robert A" sort="Edwards, Robert A" uniqKey="Edwards R" first="Robert A." last="Edwards">Robert A. Edwards</name>
<name sortKey="Olson, Robert" sort="Olson, Robert" uniqKey="Olson R" first="Robert" last="Olson">Robert Olson</name>
<name sortKey="Olson, Robert" sort="Olson, Robert" uniqKey="Olson R" first="Robert" last="Olson">Robert Olson</name>
<name sortKey="Overbeek, Ross" sort="Overbeek, Ross" uniqKey="Overbeek R" first="Ross" last="Overbeek">Ross Overbeek</name>
<name sortKey="Pusch, Gordon D" sort="Pusch, Gordon D" uniqKey="Pusch G" first="Gordon D." last="Pusch">Gordon D. Pusch</name>
<name sortKey="Pusch, Gordon D" sort="Pusch, Gordon D" uniqKey="Pusch G" first="Gordon D." last="Pusch">Gordon D. Pusch</name>
<name sortKey="Stevens, Rick" sort="Stevens, Rick" uniqKey="Stevens R" first="Rick" last="Stevens">Rick Stevens</name>
<name sortKey="Stevens, Rick" sort="Stevens, Rick" uniqKey="Stevens R" first="Rick" last="Stevens">Rick Stevens</name>
<name sortKey="Vonstein, Veronika" sort="Vonstein, Veronika" uniqKey="Vonstein V" first="Veronika" last="Vonstein">Veronika Vonstein</name>
</country>
</tree>
</affiliations>
</record>
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