Web Resources for Metagenomics Studies
Identifieur interne : 000056 ( Main/Exploration ); précédent : 000055; suivant : 000057Web Resources for Metagenomics Studies
Auteurs : Pravin Dudhagara [Inde] ; Sunil Bhavsar [Inde] ; Chintan Bhagat [Inde] ; Anjana Ghelani [Inde] ; Shreyas Bhatt [Inde] ; Rajesh Patel [Inde]Source :
- Genomics, Proteomics & Bioinformatics [ 1672-0229 ] ; 2015.
Abstract
The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for
Url:
DOI: 10.1016/j.gpb.2015.10.003
PubMed: 26602607
PubMed Central: 4678780
Affiliations:
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type="wicri:Area/Main/Curation">000056</idno><idno type="wicri:Area/Main/Exploration">000056</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Web Resources for Metagenomics Studies</title><author><name sortKey="Dudhagara, Pravin" sort="Dudhagara, Pravin" uniqKey="Dudhagara P" first="Pravin" last="Dudhagara">Pravin Dudhagara</name><affiliation wicri:level="1"><nlm:aff id="af005">Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007</wicri:regionArea><wicri:noRegion>Surat 395007</wicri:noRegion></affiliation></author><author><name sortKey="Bhavsar, Sunil" sort="Bhavsar, Sunil" uniqKey="Bhavsar S" first="Sunil" last="Bhavsar">Sunil Bhavsar</name><affiliation wicri:level="1"><nlm:aff id="af005">Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007</wicri:regionArea><wicri:noRegion>Surat 395007</wicri:noRegion></affiliation></author><author><name sortKey="Bhagat, Chintan" sort="Bhagat, Chintan" uniqKey="Bhagat C" first="Chintan" last="Bhagat">Chintan Bhagat</name><affiliation wicri:level="1"><nlm:aff id="af005">Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007</wicri:regionArea><wicri:noRegion>Surat 395007</wicri:noRegion></affiliation></author><author><name sortKey="Ghelani, Anjana" sort="Ghelani, Anjana" uniqKey="Ghelani A" first="Anjana" last="Ghelani">Anjana Ghelani</name><affiliation wicri:level="1"><nlm:aff id="af010">Department of Microbiology, Shree Ramkrishna Institute of Computer Education and Applied Sciences, Surat 395001, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Microbiology, Shree Ramkrishna Institute of Computer Education and Applied Sciences, Surat 395001</wicri:regionArea><wicri:noRegion>Surat 395001</wicri:noRegion></affiliation></author><author><name sortKey="Bhatt, Shreyas" sort="Bhatt, Shreyas" uniqKey="Bhatt S" first="Shreyas" last="Bhatt">Shreyas Bhatt</name><affiliation wicri:level="1"><nlm:aff id="af015">Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265</wicri:regionArea><wicri:noRegion>Patan 384265</wicri:noRegion></affiliation></author><author><name sortKey="Patel, Rajesh" sort="Patel, Rajesh" uniqKey="Patel R" first="Rajesh" last="Patel">Rajesh Patel</name><affiliation wicri:level="1"><nlm:aff id="af015">Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265</wicri:regionArea><wicri:noRegion>Patan 384265</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genomics, Proteomics & Bioinformatics</title><idno type="ISSN">1672-0229</idno><idno type="eISSN">2210-3244</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for <bold>metagenomics</bold> data analysis with respect to their quality and detail of analysis using simulated <bold>metagenomics</bold> data. There are at least a dozen such <bold>software tools</bold> presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using <bold>synthetic metagenome</bold>. The article comprehensively deals with the contemporary problems and the prospects of <bold>metagenomics</bold> from a bioinformatics viewpoint.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Handelsman, J" uniqKey="Handelsman J">J. Handelsman</name></author><author><name sortKey="Rondon, M R" uniqKey="Rondon M">M.R. Rondon</name></author><author><name sortKey="Brady, S F" uniqKey="Brady S">S.F. Brady</name></author><author><name sortKey="Clardy, J" uniqKey="Clardy J">J. Clardy</name></author><author><name sortKey="Goodman, R M" uniqKey="Goodman R">R.M. Goodman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daniel, R" uniqKey="Daniel R">R. 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Srinivasiah</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Dudhagara, Pravin" sort="Dudhagara, Pravin" uniqKey="Dudhagara P" first="Pravin" last="Dudhagara">Pravin Dudhagara</name></noRegion><name sortKey="Bhagat, Chintan" sort="Bhagat, Chintan" uniqKey="Bhagat C" first="Chintan" last="Bhagat">Chintan Bhagat</name><name sortKey="Bhatt, Shreyas" sort="Bhatt, Shreyas" uniqKey="Bhatt S" first="Shreyas" last="Bhatt">Shreyas Bhatt</name><name sortKey="Bhavsar, Sunil" sort="Bhavsar, Sunil" uniqKey="Bhavsar S" first="Sunil" last="Bhavsar">Sunil Bhavsar</name><name sortKey="Ghelani, Anjana" sort="Ghelani, Anjana" uniqKey="Ghelani A" first="Anjana" last="Ghelani">Anjana Ghelani</name><name sortKey="Patel, Rajesh" sort="Patel, Rajesh" uniqKey="Patel R" first="Rajesh" last="Patel">Rajesh Patel</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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