Meta4: a web application for sharing and annotating metagenomic gene predictions using web services
Identifieur interne : 000446 ( Ncbi/Checkpoint ); précédent : 000445; suivant : 000447Meta4: 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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PMC:3763215Le document en format XML
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<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>
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<author><name sortKey="Manary, M J" uniqKey="Manary M">M. J. Manary</name>
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<author><name sortKey="Trehan, I" uniqKey="Trehan I">I. Trehan</name>
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