MersV1, Ncbi, Curation, bibRecord, 000A02

Real Time Metagenomics: Using k-mers to annotate metagenomes

Identifieur interne : 000A02 ( Ncbi/Curation ); précédent : 000A01; suivant : 000A03

Real 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.

RBID : PMC:3519453

Descripteurs français

KwdFr :
- Algorithmes, Analyse de séquence d'ADN, Annotation de séquence moléculaire, Métagénome, Métagénomique ().
MESH :
- Algorithmes, Analyse de séquence d'ADN, Annotation de séquence moléculaire, Métagénome, Métagénomique.

English descriptors

KwdEn :
- Algorithms, Metagenome, Metagenomics (methods), Molecular Sequence Annotation, Sequence Analysis, DNA.
MESH :
- methods : Metagenomics.
- Algorithms, Metagenome, Molecular Sequence Annotation, Sequence Analysis, DNA.

Abstract

Summary: 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 k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-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.

Availability and implementation: This open-source application was implemented in Perl and can be accessed via a user-friendly website at http://edwards.sdsu.edu/rtmg. In addition, code to access the annotation servers is available for download from http://www.theseed.org/. FIGfams and k-mers are available for download from ftp://ftp.theseed.org/FIGfams/.

Contact:redwards@mail.sdsu.edu

Supplementary information:Supplementary data are available at Bioinformatics online.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3519453

DOI: 10.1093/bioinformatics/bts599
PubMed: 23047562
PubMed Central: 3519453

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<placeName><region type="state">Illinois</region>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Computation Institute, University of Chicago, Chicago, IL 60637</wicri:regionArea>
<placeName><region type="state">Illinois</region>
<settlement type="city">Chicago</settlement>
</placeName>
<orgName type="university">Université de Chicago</orgName>
</affiliation>
</author>
<author><name sortKey="Vonstein, Veronika" sort="Vonstein, Veronika" uniqKey="Vonstein V" first="Veronika" last="Vonstein">Veronika Vonstein</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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<author><name sortKey="Stevens, Rick" sort="Stevens, Rick" uniqKey="Stevens R" first="Rick" last="Stevens">Rick Stevens</name>
<affiliation wicri:level="2"><nlm:aff id="bts599-AFF1">Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA,</nlm:aff>
<country xml:lang="fr">États-Unis</country>
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<placeName><region type="state">Illinois</region>
<settlement type="city">Chicago</settlement>
</placeName>
<orgName type="university">Université de Chicago</orgName>
</affiliation>
</author>
<author><name sortKey="Overbeek, Ross" sort="Overbeek, Ross" uniqKey="Overbeek R" first="Ross" last="Overbeek">Ross Overbeek</name>
<affiliation wicri:level="2"><nlm:aff id="bts599-AFF1">Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA</nlm:aff>
<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>
</affiliation>
</author>
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<series><title level="j">Bioinformatics</title>
<idno type="ISSN">1367-4803</idno>
<idno type="eISSN">1367-4811</idno>
<imprint><date when="2012">2012</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Metagenome</term>
<term>Metagenomics (methods)</term>
<term>Molecular Sequence Annotation</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de séquence d'ADN</term>
<term>Annotation de séquence moléculaire</term>
<term>Métagénome</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>Metagenome</term>
<term>Molecular Sequence Annotation</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de séquence d'ADN</term>
<term>Annotation de séquence moléculaire</term>
<term>Métagénome</term>
<term>Métagénomique</term>
</keywords>
</textClass>
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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>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Angly, F E" uniqKey="Angly F">F.E. Angly</name>
</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>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Meyer, F" uniqKey="Meyer F">F. Meyer</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Overbeek, R" uniqKey="Overbeek R">R. Overbeek</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wilkening, J" uniqKey="Wilkening J">J. Wilkening</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wommack, K E" uniqKey="Wommack K">K.E. Wommack</name>
</author>
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Real Time Metagenomics: Using k-mers to annotate metagenomes

Real Time Metagenomics: Using k-mers to annotate metagenomes

Source :

Descripteurs français

English descriptors

Abstract

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