Meta4: a web application for sharing and annotating metagenomic gene predictions using web services
Identifieur interne : 000321 ( Main/Exploration ); précédent : 000320; suivant : 000322Meta4: a web application for sharing and annotating metagenomic gene predictions using web services
Auteurs : Emily J. Richardson [Royaume-Uni] ; Franck Escalettes [Royaume-Uni] ; Ian Fotheringham [Royaume-Uni] ; Robert J. Wallace [Royaume-Uni] ; Mick Watson [Royaume-Uni]Source :
- Frontiers in Genetics [ 1664-8021 ] ; 2013.
Abstract
Whole-genome shotgun metagenomics experiments produce DNA sequence data from entire ecosystems, and provide a huge amount of novel information. Gene discovery projects require up-to-date information about sequence homology and domain structure for millions of predicted proteins to be presented in a simple, easy-to-use system. There is a lack of simple, open, flexible tools that allow the rapid sharing of metagenomics datasets with collaborators in a format they can easily interrogate. We present Meta4, a flexible and extensible web application that can be used to share and annotate metagenomic gene predictions. Proteins and predicted domains are stored in a simple relational database, with a dynamic front-end which displays the results in an internet browser. Web services are used to provide up-to-date information about the proteins from homology searches against public databases. Information about Meta4 can be found on the project website
Url:
DOI: 10.3389/fgene.2013.00168
PubMed: 24046776
PubMed Central: 3763215
Affiliations:
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Richardson</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>ARK-Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh</institution><country>Easter Bush, Midlothian, UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Escalettes, Franck" sort="Escalettes, Franck" uniqKey="Escalettes F" first="Franck" last="Escalettes">Franck Escalettes</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Ingenza Ltd., Roslin BioCentre</institution><country>Midlothian, UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Fotheringham, Ian" sort="Fotheringham, Ian" uniqKey="Fotheringham I" first="Ian" last="Fotheringham">Ian Fotheringham</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Ingenza Ltd., Roslin BioCentre</institution><country>Midlothian, UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Wallace, Robert J" sort="Wallace, Robert J" uniqKey="Wallace R" first="Robert J." last="Wallace">Robert J. Wallace</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Rowett Institute of Nutrition and Health, University of Aberdeen</institution><country>Aberdeen, UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Watson, Mick" sort="Watson, Mick" uniqKey="Watson M" first="Mick" last="Watson">Mick Watson</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>ARK-Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh</institution><country>Easter Bush, Midlothian, UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Edinburgh Genomics, University of Edinburgh</institution><country>Edinburgh, UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Genetics</title><idno type="eISSN">1664-8021</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Whole-genome shotgun metagenomics experiments produce DNA sequence data from entire ecosystems, and provide a huge amount of novel information. Gene discovery projects require up-to-date information about sequence homology and domain structure for millions of predicted proteins to be presented in a simple, easy-to-use system. There is a lack of simple, open, flexible tools that allow the rapid sharing of metagenomics datasets with collaborators in a format they can easily interrogate. We present Meta4, a flexible and extensible web application that can be used to share and annotate metagenomic gene predictions. Proteins and predicted domains are stored in a simple relational database, with a dynamic front-end which displays the results in an internet browser. Web services are used to provide up-to-date information about the proteins from homology searches against public databases. Information about Meta4 can be found on the project website<sup><xref ref-type="fn" rid="fn01">1</xref></sup>, code is available on Github<sup><xref ref-type="fn" rid="fn02">2</xref></sup>, a cloud image is available, and an example implementation can be seen at <ext-link ext-link-type="uri" xlink:href="http://www.ark-genomics.org/tools/meta4"></ext-link></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Afgan, E" uniqKey="Afgan E">E. Afgan</name></author><author><name sortKey="Chapman, B" uniqKey="Chapman B">B. Chapman</name></author><author><name sortKey="Jadan, M" uniqKey="Jadan M">M. Jadan</name></author><author><name sortKey="Franke, V" uniqKey="Franke V">V. Franke</name></author><author><name sortKey="Taylor, J" uniqKey="Taylor J">J. Taylor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Boisvert, S" uniqKey="Boisvert S">S. 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Rey</name></author><author><name sortKey="Manary, M J" uniqKey="Manary M">M. J. Manary</name></author><author><name sortKey="Trehan, I" uniqKey="Trehan I">I. Trehan</name></author><author><name sortKey="Dominguez Bello, M G" uniqKey="Dominguez Bello M">M. G. Dominguez-Bello</name></author><author><name sortKey="Contreras, M" uniqKey="Contreras M">M. Contreras</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yok, N G" uniqKey="Yok N">N. G. Yok</name></author><author><name sortKey="Rosen, G L" uniqKey="Rosen G">G. L. Rosen</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Royaume-Uni</li></country></list><tree><country name="Royaume-Uni"><noRegion><name sortKey="Richardson, Emily J" sort="Richardson, Emily J" uniqKey="Richardson E" first="Emily J." last="Richardson">Emily J. Richardson</name></noRegion><name sortKey="Escalettes, Franck" sort="Escalettes, Franck" uniqKey="Escalettes F" first="Franck" last="Escalettes">Franck Escalettes</name><name sortKey="Fotheringham, Ian" sort="Fotheringham, Ian" uniqKey="Fotheringham I" first="Ian" last="Fotheringham">Ian Fotheringham</name><name sortKey="Wallace, Robert J" sort="Wallace, Robert J" uniqKey="Wallace R" first="Robert J." last="Wallace">Robert J. Wallace</name><name sortKey="Watson, Mick" sort="Watson, Mick" uniqKey="Watson M" first="Mick" last="Watson">Mick Watson</name><name sortKey="Watson, Mick" sort="Watson, Mick" uniqKey="Watson M" first="Mick" last="Watson">Mick Watson</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|type= RBID
|clé= PMC:3763215
|texte= Meta4: a web application for sharing and annotating metagenomic gene predictions using web services
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:24046776" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |