Meta4: a web application for sharing and annotating metagenomic gene predictions using web services
Identifieur interne : 000528 ( Pmc/Curation ); précédent : 000527; suivant : 000529Meta4: 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
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000528
Links to Exploration step
PMC:3763215Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Meta4: a web application for sharing and annotating metagenomic gene predictions using web services</title><author><name sortKey="Richardson, Emily J" sort="Richardson, Emily J" uniqKey="Richardson E" first="Emily J." last="Richardson">Emily J. 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></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24046776</idno><idno type="pmc">3763215</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763215</idno><idno type="RBID">PMC:3763215</idno><idno type="doi">10.3389/fgene.2013.00168</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000528</idno><idno type="wicri:Area/Pmc/Curation">000528</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Meta4: a web application for sharing and annotating metagenomic gene predictions using web services</title><author><name sortKey="Richardson, Emily J" sort="Richardson, Emily J" uniqKey="Richardson E" first="Emily J." last="Richardson">Emily J. 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. Boisvert</name></author><author><name sortKey="Raymond, F" uniqKey="Raymond F">F. Raymond</name></author><author><name sortKey="Godzaridis, E" uniqKey="Godzaridis E">E. Godzaridis</name></author><author><name sortKey="Laviolette, F" uniqKey="Laviolette F">F. Laviolette</name></author><author><name sortKey="Corbeil, J" uniqKey="Corbeil J">J. Corbeil</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cowan, D" uniqKey="Cowan D">D. Cowan</name></author><author><name sortKey="Meyer, Q" uniqKey="Meyer Q">Q. Meyer</name></author><author><name sortKey="Stafford, W" uniqKey="Stafford W">W. Stafford</name></author><author><name sortKey="Muyanga, S" uniqKey="Muyanga S">S. Muyanga</name></author><author><name sortKey="Cameron, R" uniqKey="Cameron R">R. Cameron</name></author><author><name sortKey="Wittwer, P" uniqKey="Wittwer P">P. Wittwer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cowan, D A" uniqKey="Cowan D">D. A. Cowan</name></author><author><name sortKey="Arslanoglu, A" uniqKey="Arslanoglu A">A. Arslanoglu</name></author><author><name sortKey="Burton, S G" uniqKey="Burton S">S. G. Burton</name></author><author><name sortKey="Baker, G C" uniqKey="Baker G">G. C. Baker</name></author><author><name sortKey="Cameron, R A" uniqKey="Cameron R">R. A. Cameron</name></author><author><name sortKey="Smith, J J" uniqKey="Smith J">J. J. Smith</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eddy, S R" uniqKey="Eddy S">S. R. Eddy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hess, M" uniqKey="Hess M">M. Hess</name></author><author><name sortKey="Sczyrba, A" uniqKey="Sczyrba A">A. Sczyrba</name></author><author><name sortKey="Egan, R" uniqKey="Egan R">R. Egan</name></author><author><name sortKey="Kim, T W" uniqKey="Kim T">T. W. Kim</name></author><author><name sortKey="Chokhawala, H" uniqKey="Chokhawala H">H. Chokhawala</name></author><author><name sortKey="Schroth, G" uniqKey="Schroth G">G. Schroth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hoff, K J" uniqKey="Hoff K">K. J. Hoff</name></author><author><name sortKey="Lingner, T" uniqKey="Lingner T">T. Lingner</name></author><author><name sortKey="Meinicke, P" uniqKey="Meinicke P">P. Meinicke</name></author><author><name sortKey="Tech, M" uniqKey="Tech M">M. Tech</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jain, E" uniqKey="Jain E">E. Jain</name></author><author><name sortKey="Bairoch, A" uniqKey="Bairoch A">A. Bairoch</name></author><author><name sortKey="Duvaud, S" uniqKey="Duvaud S">S. Duvaud</name></author><author><name sortKey="Phan, I" uniqKey="Phan I">I. Phan</name></author><author><name sortKey="Redaschi, N" uniqKey="Redaschi N">N. Redaschi</name></author><author><name sortKey="Suzek, B E" uniqKey="Suzek B">B. E. Suzek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kelley, D R" uniqKey="Kelley D">D. R. Kelley</name></author><author><name sortKey="Liu, B" uniqKey="Liu B">B. Liu</name></author><author><name sortKey="Delcher, A L" uniqKey="Delcher A">A. L. Delcher</name></author><author><name sortKey="Pop, M" uniqKey="Pop M">M. Pop</name></author><author><name sortKey="Salzberg, S L" uniqKey="Salzberg S">S. L. Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, R" uniqKey="Li R">R. Li</name></author><author><name sortKey="Zhu, H" uniqKey="Zhu H">H. Zhu</name></author><author><name sortKey="Ruan, J" uniqKey="Ruan J">J. Ruan</name></author><author><name sortKey="Qian, W" uniqKey="Qian W">W. Qian</name></author><author><name sortKey="Fang, X" uniqKey="Fang X">X. Fang</name></author><author><name sortKey="Shi, Z" uniqKey="Shi Z">Z. Shi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mackelprang, R" uniqKey="Mackelprang R">R. Mackelprang</name></author><author><name sortKey="Waldrop, M P" uniqKey="Waldrop M">M. P. Waldrop</name></author><author><name sortKey="Deangelis, K M" uniqKey="Deangelis K">K. M. Deangelis</name></author><author><name sortKey="David, M M" uniqKey="David M">M. M. David</name></author><author><name sortKey="Chavarria, K L" uniqKey="Chavarria K">K. L. Chavarria</name></author><author><name sortKey="Blazewicz, S J" uniqKey="Blazewicz S">S. J. Blazewicz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Magrane, M" uniqKey="Magrane M">M. Magrane</name></author><author><name sortKey="Consortium, U" uniqKey="Consortium U">U. Consortium</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Markowitz, V M" uniqKey="Markowitz V">V. M. Markowitz</name></author><author><name sortKey="Chen, I M" uniqKey="Chen I">I. M. Chen</name></author><author><name sortKey="Chu, K" uniqKey="Chu K">K. Chu</name></author><author><name sortKey="Szeto, E" uniqKey="Szeto E">E. Szeto</name></author><author><name sortKey="Palaniappan, K" uniqKey="Palaniappan K">K. Palaniappan</name></author><author><name sortKey="Grechkin, Y" uniqKey="Grechkin Y">Y. Grechkin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcwilliam, H" uniqKey="Mcwilliam H">H. McWilliam</name></author><author><name sortKey="Valentin, F" uniqKey="Valentin F">F. Valentin</name></author><author><name sortKey="Goujon, M" uniqKey="Goujon M">M. Goujon</name></author><author><name sortKey="Li, W" uniqKey="Li W">W. Li</name></author><author><name sortKey="Narayanasamy, M" uniqKey="Narayanasamy M">M. Narayanasamy</name></author><author><name sortKey="Martin, J" uniqKey="Martin J">J. Martin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meyer, F" uniqKey="Meyer F">F. Meyer</name></author><author><name sortKey="Paarmann, D" uniqKey="Paarmann D">D. Paarmann</name></author><author><name sortKey="D Ouza, M" uniqKey="D Ouza M">M. D’souza</name></author><author><name sortKey="Olson, R" uniqKey="Olson R">R. Olson</name></author><author><name sortKey="Glass, E M" uniqKey="Glass E">E. M. Glass</name></author><author><name sortKey="Kubal, M" uniqKey="Kubal M">M. Kubal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mulder, N" uniqKey="Mulder N">N. Mulder</name></author><author><name sortKey="Apweiler, R" uniqKey="Apweiler R">R. Apweiler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Namiki, T" uniqKey="Namiki T">T. Namiki</name></author><author><name sortKey="Hachiya, T" uniqKey="Hachiya T">T. Hachiya</name></author><author><name sortKey="Tanaka, H" uniqKey="Tanaka H">H. Tanaka</name></author><author><name sortKey="Sakakibara, Y" uniqKey="Sakakibara Y">Y. Sakakibara</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Noguchi, H" uniqKey="Noguchi H">H. Noguchi</name></author><author><name sortKey="Taniguchi, T" uniqKey="Taniguchi T">T. Taniguchi</name></author><author><name sortKey="Itoh, T" uniqKey="Itoh T">T. Itoh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pell, J" uniqKey="Pell J">J. Pell</name></author><author><name sortKey="Hintze, A" uniqKey="Hintze A">A. Hintze</name></author><author><name sortKey="Canino Koning, R" uniqKey="Canino Koning R">R. Canino-Koning</name></author><author><name sortKey="Howe, A" uniqKey="Howe A">A. Howe</name></author><author><name sortKey="Tiedje, J M" uniqKey="Tiedje J">J. M. Tiedje</name></author><author><name sortKey="Brown, C T" uniqKey="Brown C">C. T. Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peng, Y" uniqKey="Peng Y">Y. Peng</name></author><author><name sortKey="Leung, H C" uniqKey="Leung H">H. C. Leung</name></author><author><name sortKey="Yiu, S M" uniqKey="Yiu S">S. M. Yiu</name></author><author><name sortKey="Chin, F Y" uniqKey="Chin F">F. Y. Chin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Punta, M" uniqKey="Punta M">M. Punta</name></author><author><name sortKey="Coggill, P C" uniqKey="Coggill P">P. C. Coggill</name></author><author><name sortKey="Eberhardt, R Y" uniqKey="Eberhardt R">R. Y. Eberhardt</name></author><author><name sortKey="Mistry, J" uniqKey="Mistry J">J. Mistry</name></author><author><name sortKey="Tate, J" uniqKey="Tate J">J. Tate</name></author><author><name sortKey="Boursnell, C" uniqKey="Boursnell C">C. Boursnell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rho, M" uniqKey="Rho M">M. Rho</name></author><author><name sortKey="Tang, H" uniqKey="Tang H">H. Tang</name></author><author><name sortKey="Ye, Y" uniqKey="Ye Y">Y. Ye</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Richardson, E J" uniqKey="Richardson E">E. J. Richardson</name></author><author><name sortKey="Watson, M" uniqKey="Watson M">M. Watson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sigrist, C J" uniqKey="Sigrist C">C. J. Sigrist</name></author><author><name sortKey="Cerutti, L" uniqKey="Cerutti L">L. Cerutti</name></author><author><name sortKey="De Castro, E" uniqKey="De Castro E">E. De Castro</name></author><author><name sortKey="Langendijk Genevaux, P S" uniqKey="Langendijk Genevaux P">P. S. Langendijk-Genevaux</name></author><author><name sortKey="Bulliard, V" uniqKey="Bulliard V">V. Bulliard</name></author><author><name sortKey="Bairoch, A" uniqKey="Bairoch A">A. Bairoch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sun, S" uniqKey="Sun S">S. Sun</name></author><author><name sortKey="Chen, J" uniqKey="Chen J">J. Chen</name></author><author><name sortKey="Li, W" uniqKey="Li W">W. Li</name></author><author><name sortKey="Altintas, I" uniqKey="Altintas I">I. Altintas</name></author><author><name sortKey="Lin, A" uniqKey="Lin A">A. Lin</name></author><author><name sortKey="Peltier, S" uniqKey="Peltier S">S. Peltier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Treangen, T J" uniqKey="Treangen T">T. J. Treangen</name></author><author><name sortKey="Koren, S" uniqKey="Koren S">S. Koren</name></author><author><name sortKey="Sommer, D D" uniqKey="Sommer D">D. D. Sommer</name></author><author><name sortKey="Liu, B" uniqKey="Liu B">B. Liu</name></author><author><name sortKey="Astrovskaya, I" uniqKey="Astrovskaya I">I. Astrovskaya</name></author><author><name sortKey="Ondov, B" uniqKey="Ondov B">B. Ondov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Venter, J C" uniqKey="Venter J">J. C. Venter</name></author><author><name sortKey="Remington, K" uniqKey="Remington K">K. Remington</name></author><author><name sortKey="Heidelberg, J F" uniqKey="Heidelberg J">J. F. Heidelberg</name></author><author><name sortKey="Halpern, A L" uniqKey="Halpern A">A. L. Halpern</name></author><author><name sortKey="Rusch, D" uniqKey="Rusch D">D. Rusch</name></author><author><name sortKey="Eisen, J A" uniqKey="Eisen J">J. A. Eisen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yatsunenko, T" uniqKey="Yatsunenko T">T. Yatsunenko</name></author><author><name sortKey="Rey, F E" uniqKey="Rey F">F. E. 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><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Genet</journal-id><journal-id journal-id-type="iso-abbrev">Front Genet</journal-id><journal-id journal-id-type="publisher-id">Front. Genet.</journal-id><journal-title-group><journal-title>Frontiers in Genetics</journal-title></journal-title-group><issn pub-type="epub">1664-8021</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24046776</article-id><article-id pub-id-type="pmc">3763215</article-id><article-id pub-id-type="doi">10.3389/fgene.2013.00168</article-id><article-categories><subj-group subj-group-type="heading"><subject>Genetics</subject><subj-group><subject>Methods Article</subject></subj-group></subj-group></article-categories><title-group><article-title>Meta4: a web application for sharing and annotating metagenomic gene predictions using web services</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Richardson</surname><given-names>Emily J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Escalettes</surname><given-names>Franck</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fotheringham</surname><given-names>Ian</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wallace</surname><given-names>Robert J.</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Watson</surname><given-names>Mick</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>ARK-Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh</institution><country>Easter Bush, Midlothian, UK</country></aff><aff id="aff2"><sup>2</sup><institution>Ingenza Ltd., Roslin BioCentre</institution><country>Midlothian, UK</country></aff><aff id="aff3"><sup>3</sup><institution>Rowett Institute of Nutrition and Health, University of Aberdeen</institution><country>Aberdeen, UK</country></aff><aff id="aff4"><sup>4</sup><institution>Edinburgh Genomics, University of Edinburgh</institution><country>Edinburgh, UK</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: <italic>John Hancock, University of Cambridge, UK</italic></p></fn><fn fn-type="edited-by"><p>Reviewed by: <italic>Ugur Sezerman, Sabanci University, Turkey; Pascale Gaudet, Swiss Institute of Bioinformatics, Switzerland</italic></p></fn><corresp id="fn001">*Correspondence: <italic>Mick Watson, ARK-Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Division of Genetics and Genomics, Easter Bush, Midlothian EH25 9RG, UK e-mail: <email xlink:type="simple">mick.watson@roslin.ed.ac.uk</email></italic></corresp><fn fn-type="other" id="fn002"><p>This article was submitted to Bioinformatics and Computational Biology, a section of the journal Frontiers in Genetics.</p></fn></author-notes><pub-date pub-type="epub"><day>05</day><month>9</month><year>2013</year></pub-date><pub-date pub-type="collection"><year>2013</year></pub-date><volume>4</volume><elocation-id>168</elocation-id><history><date date-type="received"><day>01</day><month>5</month><year>2013</year></date><date date-type="accepted"><day>13</day><month>8</month><year>2013</year></date></history><permissions><copyright-statement>Copyright © Richardson, Escalettes, Fotheringham,Wallace andWatson.</copyright-statement><copyright-year>2013</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p> This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><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></abstract><kwd-group><kwd>metagenomics</kwd><kwd>database</kwd><kwd>web service</kwd><kwd>gene discovery</kwd><kwd>bioinformatics</kwd></kwd-group><counts><fig-count count="2"></fig-count><table-count count="0"></table-count><equation-count count="0"></equation-count><ref-count count="29"></ref-count><page-count count="6"></page-count><word-count count="0"></word-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Pmc/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000528 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd -nk 000528 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Ticri/CIDE
|area= CyberinfraV1
|flux= Pmc
|étape= Curation
|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/Pmc/Curation/RBID.i -Sk "pubmed:24046776" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |