Web Resources for Metagenomics Studies
Identifieur interne : 000692 ( Ncbi/Merge ); précédent : 000691; suivant : 000693Web 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
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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 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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></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26602607</idno><idno type="pmc">4678780</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678780</idno><idno type="RBID">PMC:4678780</idno><idno type="doi">10.1016/j.gpb.2015.10.003</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000706</idno><idno type="wicri:Area/Pmc/Curation">000706</idno><idno type="wicri:Area/Pmc/Checkpoint">000051</idno><idno type="wicri:Area/Ncbi/Merge">000692</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. Daniel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thomas, T" uniqKey="Thomas T">T. Thomas</name></author><author><name sortKey="Gilbert, J" uniqKey="Gilbert J">J. Gilbert</name></author><author><name sortKey="Meyer, F" uniqKey="Meyer F">F. Meyer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dudhagara, P" uniqKey="Dudhagara P">P. Dudhagara</name></author><author><name sortKey="Ghelani, A" uniqKey="Ghelani A">A. Ghelani</name></author><author><name sortKey="Patel, R" uniqKey="Patel R">R. Patel</name></author><author><name sortKey="Chaudhari, R" uniqKey="Chaudhari R">R. Chaudhari</name></author><author><name sortKey="Bhatt, S" uniqKey="Bhatt S">S. Bhatt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ghelani, A" uniqKey="Ghelani A">A. Ghelani</name></author><author><name sortKey="Patel, R" uniqKey="Patel R">R. Patel</name></author><author><name sortKey="Mangrola, A" uniqKey="Mangrola A">A. Mangrola</name></author><author><name sortKey="Dudhagara, P" uniqKey="Dudhagara P">P. Dudhagara</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dudhagara, P" uniqKey="Dudhagara P">P. Dudhagara</name></author><author><name sortKey="Ghelani, A" uniqKey="Ghelani A">A. Ghelani</name></author><author><name sortKey="Bhavsar, S" uniqKey="Bhavsar S">S. Bhavsar</name></author><author><name sortKey="Bhatt, S" uniqKey="Bhatt S">S. Bhatt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carlos, N" uniqKey="Carlos N">N. Carlos</name></author><author><name sortKey="Tang, Y W" uniqKey="Tang Y">Y.W. Tang</name></author><author><name sortKey="Pei, Z" uniqKey="Pei Z">Z. Pei</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oulas, A" uniqKey="Oulas A">A. Oulas</name></author><author><name sortKey="Pavloudi, C" uniqKey="Pavloudi C">C. Pavloudi</name></author><author><name sortKey="Polymenakou, P" uniqKey="Polymenakou P">P. Polymenakou</name></author><author><name sortKey="Pavlopoulos, G A" uniqKey="Pavlopoulos G">G.A. Pavlopoulos</name></author><author><name sortKey="Papanikolaou, N" uniqKey="Papanikolaou N">N. Papanikolaou</name></author><author><name sortKey="Kotoulas, G" uniqKey="Kotoulas G">G. Kotoulas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Patel, R" uniqKey="Patel R">R. Patel</name></author><author><name sortKey="Mevada, V" uniqKey="Mevada V">V. Mevada</name></author><author><name sortKey="Prajapati, D" uniqKey="Prajapati D">D. Prajapati</name></author><author><name sortKey="Dudhagara, P" uniqKey="Dudhagara P">P. Dudhagara</name></author><author><name sortKey="Koringa, P" uniqKey="Koringa P">P. Koringa</name></author><author><name sortKey="Joshi, C G" uniqKey="Joshi C">C.G. Joshi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mangrola, A V" uniqKey="Mangrola A">A.V. Mangrola</name></author><author><name sortKey="Dudhagara, P" uniqKey="Dudhagara P">P. Dudhagara</name></author><author><name sortKey="Koringa, P" uniqKey="Koringa P">P. Koringa</name></author><author><name sortKey="Joshi, C G" uniqKey="Joshi C">C.G. Joshi</name></author><author><name sortKey="Patel, R K" uniqKey="Patel R">R.K. Patel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Singh, A H" uniqKey="Singh A">A.H. Singh</name></author><author><name sortKey="Doerks, T" uniqKey="Doerks T">T. Doerks</name></author><author><name sortKey="Letunic, I" uniqKey="Letunic I">I. Letunic</name></author><author><name sortKey="Raes, J" uniqKey="Raes J">J. Raes</name></author><author><name sortKey="Bork, P" uniqKey="Bork P">P. Bork</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ounit, R" uniqKey="Ounit R">R. Ounit</name></author><author><name sortKey="Wanamaker, S" uniqKey="Wanamaker S">S. Wanamaker</name></author><author><name sortKey="Close, T J" uniqKey="Close T">T.J. Close</name></author><author><name sortKey="Lonardi, S" uniqKey="Lonardi S">S. Lonardi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mandal, R S" uniqKey="Mandal R">R.S. Mandal</name></author><author><name sortKey="Saha, S" uniqKey="Saha S">S. Saha</name></author><author><name sortKey="Das, S" uniqKey="Das S">S. Das</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Behnam, E" uniqKey="Behnam E">E. Behnam</name></author><author><name sortKey="Smith, A D" uniqKey="Smith A">A.D. Smith</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Overbeek, R" uniqKey="Overbeek R">R. Overbeek</name></author><author><name sortKey="Begley, T" uniqKey="Begley T">T. Begley</name></author><author><name sortKey="Butler, R M" uniqKey="Butler R">R.M. Butler</name></author><author><name sortKey="Choudhuri, J V" uniqKey="Choudhuri J">J.V. Choudhuri</name></author><author><name sortKey="Chuang, H Y" uniqKey="Chuang H">H.Y. Chuang</name></author><author><name sortKey="Cohoon, M" uniqKey="Cohoon M">M. Cohoon</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="Overbeek, R" uniqKey="Overbeek R">R. Overbeek</name></author><author><name sortKey="Olson, R" uniqKey="Olson R">R. Olson</name></author><author><name sortKey="Pusch, G D" uniqKey="Pusch G">G.D. Pusch</name></author><author><name sortKey="Olsen, G J" uniqKey="Olsen G">G.J. Olsen</name></author><author><name sortKey="Davis, J J" uniqKey="Davis J">J.J. Davis</name></author><author><name sortKey="Disz, T" uniqKey="Disz T">T. Disz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wilke, A" uniqKey="Wilke A">A. Wilke</name></author><author><name sortKey="Bischof, J" uniqKey="Bischof J">J. Bischof</name></author><author><name sortKey="Harrison, T" uniqKey="Harrison T">T. Harrison</name></author><author><name sortKey="Brettin, T" uniqKey="Brettin T">T. Brettin</name></author><author><name sortKey="D Ouza, M" uniqKey="D Ouza M">M. D’Souza</name></author><author><name sortKey="Gerlach, W" uniqKey="Gerlach W">W. Gerlach</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sun, Q" uniqKey="Sun Q">Q. Sun</name></author><author><name sortKey="Liu, L" uniqKey="Liu L">L. Liu</name></author><author><name sortKey="Wu, L" uniqKey="Wu L">L. Wu</name></author><author><name sortKey="Li, W" uniqKey="Li W">W. Li</name></author><author><name sortKey="Liu, Q" uniqKey="Liu Q">Q. Liu</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Markowitz, V M" uniqKey="Markowitz V">V.M. Markowitz</name></author><author><name sortKey="Ivanova, N N" uniqKey="Ivanova N">N.N. Ivanova</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="Chu, K" uniqKey="Chu K">K. Chu</name></author><author><name sortKey="Dalevi, D" uniqKey="Dalevi D">D. Dalevi</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="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="Pillay, M" uniqKey="Pillay M">M. Pillay</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="Palaniappan, K" uniqKey="Palaniappan K">K. Palaniappan</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="Grechkin, Y" uniqKey="Grechkin Y">Y. Grechkin</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="Jacob, B" uniqKey="Jacob B">B. Jacob</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goll, J" uniqKey="Goll J">J. Goll</name></author><author><name sortKey="Rusch, D B" uniqKey="Rusch D">D.B. Rusch</name></author><author><name sortKey="Tanenbaum, D M" uniqKey="Tanenbaum D">D.M. Tanenbaum</name></author><author><name sortKey="Thiagarajan, M" uniqKey="Thiagarajan M">M. Thiagarajan</name></author><author><name sortKey="Li, K" uniqKey="Li K">K. Li</name></author><author><name sortKey="Methe, B A" uniqKey="Methe B">B.A. Methe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goll, J" uniqKey="Goll J">J. Goll</name></author><author><name sortKey="Thiagarajan, M" uniqKey="Thiagarajan M">M. Thiagarajan</name></author><author><name sortKey="Abubucker, S" uniqKey="Abubucker S">S. Abubucker</name></author><author><name sortKey="Huttenhower, C" uniqKey="Huttenhower C">C. Huttenhower</name></author><author><name sortKey="Yooseph, S" uniqKey="Yooseph S">S. Yooseph</name></author><author><name sortKey="Methe, B A" uniqKey="Methe B">B.A. Methé</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lingner, T" uniqKey="Lingner T">T. Lingner</name></author><author><name sortKey="Asshauer, K P" uniqKey="Asshauer K">K.P. Asshauer</name></author><author><name sortKey="Schreiber, F" uniqKey="Schreiber F">F. Schreiber</name></author><author><name sortKey="Meinicke, P" uniqKey="Meinicke P">P. Meinicke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Arndt, D" uniqKey="Arndt D">D. Arndt</name></author><author><name sortKey="Xia, J" uniqKey="Xia J">J. Xia</name></author><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y. Liu</name></author><author><name sortKey="Zhou, Y" uniqKey="Zhou Y">Y. Zhou</name></author><author><name sortKey="Guo, A C" uniqKey="Guo A">A.C. Guo</name></author><author><name sortKey="Cruz, J A" uniqKey="Cruz J">J.A. Cruz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Su, C H" uniqKey="Su C">C.H. Su</name></author><author><name sortKey="Hsu, M T" uniqKey="Hsu M">M.T. Hsu</name></author><author><name sortKey="Wang, T Y" uniqKey="Wang T">T.Y. Wang</name></author><author><name sortKey="Chiang, S" uniqKey="Chiang S">S. Chiang</name></author><author><name sortKey="Cheng, J H" uniqKey="Cheng J">J.H. Cheng</name></author><author><name sortKey="Weng, F C" uniqKey="Weng F">F.C. Weng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Luo, C" uniqKey="Luo C">C. Luo</name></author><author><name sortKey="Rodriguez R, L M" uniqKey="Rodriguez R L">L.M. Rodriguez-R</name></author><author><name sortKey="Konstantinidis, K T" uniqKey="Konstantinidis K">K.T. Konstantinidis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chivian, D" uniqKey="Chivian D">D. Chivian</name></author><author><name sortKey="Dehal, P S" uniqKey="Dehal P">P.S. Dehal</name></author><author><name sortKey="Keller, K" uniqKey="Keller K">K. Keller</name></author><author><name sortKey="Arkin, A P" uniqKey="Arkin A">A.P. Arkin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dehal, P S" uniqKey="Dehal P">P.S. Dehal</name></author><author><name sortKey="Joachimiak, M P" uniqKey="Joachimiak M">M.P. Joachimiak</name></author><author><name sortKey="Price, M N" uniqKey="Price M">M.N. Price</name></author><author><name sortKey="Bates, J T" uniqKey="Bates J">J.T. Bates</name></author><author><name sortKey="Baumohl, J K" uniqKey="Baumohl J">J.K. Baumohl</name></author><author><name sortKey="Chivian, D" uniqKey="Chivian D">D. Chivian</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hunter, S" uniqKey="Hunter S">S. Hunter</name></author><author><name sortKey="Corbett, M" uniqKey="Corbett M">M. Corbett</name></author><author><name sortKey="Denise, H" uniqKey="Denise H">H. Denise</name></author><author><name sortKey="Fraser, M" uniqKey="Fraser M">M. Fraser</name></author><author><name sortKey="Gonzalez Beltran, A" uniqKey="Gonzalez Beltran A">A. Gonzalez-Beltran</name></author><author><name sortKey="Hunter, C" uniqKey="Hunter C">C. Hunter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Seshadri, R" uniqKey="Seshadri R">R. Seshadri</name></author><author><name sortKey="Kravitz, S A" uniqKey="Kravitz S">S.A. Kravitz</name></author><author><name sortKey="Smarr, L" uniqKey="Smarr L">L. Smarr</name></author><author><name sortKey="Gilna, P" uniqKey="Gilna P">P. Gilna</name></author><author><name sortKey="Frazier, M" uniqKey="Frazier M">M. Frazier</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="Roux, S" uniqKey="Roux S">S. Roux</name></author><author><name sortKey="Faubladier, M" uniqKey="Faubladier M">M. Faubladier</name></author><author><name sortKey="Mahul, A" uniqKey="Mahul A">A. Mahul</name></author><author><name sortKey="Paulhe, N" uniqKey="Paulhe N">N. Paulhe</name></author><author><name sortKey="Bernard, A" uniqKey="Bernard A">A. Bernard</name></author><author><name sortKey="Debroas, D" uniqKey="Debroas D">D. Debroas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Roux, S" uniqKey="Roux S">S. Roux</name></author><author><name sortKey="Tournayre, J" uniqKey="Tournayre J">J. Tournayre</name></author><author><name sortKey="Mahul, A" uniqKey="Mahul A">A. Mahul</name></author><author><name sortKey="Debroas, D" uniqKey="Debroas D">D. Debroas</name></author><author><name sortKey="Enault, F" uniqKey="Enault F">F. Enault</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wommack, K E" uniqKey="Wommack K">K.E. Wommack</name></author><author><name sortKey="Bhavsar, J" uniqKey="Bhavsar J">J. Bhavsar</name></author><author><name sortKey="Polson, S W" uniqKey="Polson S">S.W. Polson</name></author><author><name sortKey="Chen, J" uniqKey="Chen J">J. Chen</name></author><author><name sortKey="Dumas, M" uniqKey="Dumas M">M. Dumas</name></author><author><name sortKey="Srinivasiah, S" uniqKey="Srinivasiah S">S. Srinivasiah</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="review-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genomics Proteomics Bioinformatics</journal-id><journal-id journal-id-type="iso-abbrev">Genomics Proteomics Bioinformatics</journal-id><journal-title-group><journal-title>Genomics, Proteomics & Bioinformatics</journal-title></journal-title-group><issn pub-type="ppub">1672-0229</issn><issn pub-type="epub">2210-3244</issn><publisher><publisher-name>Elsevier</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26602607</article-id><article-id pub-id-type="pmc">4678780</article-id><article-id pub-id-type="publisher-id">S1672-0229(15)00142-4</article-id><article-id pub-id-type="doi">10.1016/j.gpb.2015.10.003</article-id><article-categories><subj-group subj-group-type="heading"><subject>Resource Review</subject></subj-group></article-categories><title-group><article-title>Web Resources for Metagenomics Studies</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Dudhagara</surname><given-names>Pravin</given-names></name><email>dudhagarapr@gmail.com</email><xref rid="af005" ref-type="aff">1</xref><xref rid="cor1" ref-type="corresp">⁎</xref><xref rid="fn1" ref-type="fn">a</xref></contrib><contrib contrib-type="author"><name><surname>Bhavsar</surname><given-names>Sunil</given-names></name><xref rid="af005" ref-type="aff">1</xref><xref rid="fn2" ref-type="fn">b</xref></contrib><contrib contrib-type="author"><name><surname>Bhagat</surname><given-names>Chintan</given-names></name><xref rid="af005" ref-type="aff">1</xref><xref rid="fn3" ref-type="fn">c</xref></contrib><contrib contrib-type="author"><name><surname>Ghelani</surname><given-names>Anjana</given-names></name><xref rid="af010" ref-type="aff">2</xref><xref rid="fn4" ref-type="fn">d</xref></contrib><contrib contrib-type="author"><name><surname>Bhatt</surname><given-names>Shreyas</given-names></name><xref rid="af015" ref-type="aff">3</xref><xref rid="fn5" ref-type="fn">e</xref></contrib><contrib contrib-type="author"><name><surname>Patel</surname><given-names>Rajesh</given-names></name><xref rid="af015" ref-type="aff">3</xref><xref rid="fn6" ref-type="fn">f</xref></contrib></contrib-group><aff id="af005"><label>1</label>Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India</aff><aff id="af010"><label>2</label>Department of Microbiology, Shree Ramkrishna Institute of Computer Education and Applied Sciences, Surat 395001, India</aff><aff id="af015"><label>3</label>Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265, India</aff><author-notes><corresp id="cor1"><label>⁎</label>Corresponding author. <email>dudhagarapr@gmail.com</email></corresp><fn id="fn1"><label>a</label><p>ORCID: 0000-0002-4041-6751.</p></fn><fn id="fn2"><label>b</label><p>ORCID: 0000-0002-7525-0624.</p></fn><fn id="fn3"><label>c</label><p>ORCID: 0000-0002-2318-5998.</p></fn><fn id="fn4"><label>d</label><p>ORCID: 0000-0003-4638-6925.</p></fn><fn id="fn5"><label>e</label><p>ORCID: 0000-0002-4364-2244.</p></fn><fn id="fn6"><label>f</label><p>ORCID: 0000-0002-4712-1921.</p></fn></author-notes><pub-date pub-type="pmc-release"><day>18</day><month>11</month><year>2015</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>10</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>18</day><month>11</month><year>2015</year></pub-date><volume>13</volume><issue>5</issue><fpage>296</fpage><lpage>303</lpage><history><date date-type="received"><day>6</day><month>8</month><year>2015</year></date><date date-type="rev-recd"><day>9</day><month>10</month><year>2015</year></date><date date-type="accepted"><day>13</day><month>10</month><year>2015</year></date></history><permissions><copyright-statement>© 2015 The Authors. Production and hosting by Elsevier B.V. on behalf of Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China.</copyright-statement><copyright-year>2015</copyright-year><copyright-holder></copyright-holder><license license-type="CC BY" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).</license-p></license></permissions><abstract><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></abstract><kwd-group><title>Keywords</title><kwd>Metagenomics</kwd><kwd>Metagenomes</kwd><kwd>Web resources</kwd><kwd>Software tools</kwd><kwd>Synthetic metagenome</kwd></kwd-group></article-meta><notes><p id="ms005">Handled by Vladimir B. Bajic</p></notes></front><floats-group><fig id="f0005"><label>Figure 1</label><caption><p><bold>Relative citation of the metagenomics software tools from articles published in peer-reviewed scientific journals by October 2015</bold></p><p>Year in the bracket in the legend box indicates the year of original release of the respective tool. Citation of each tool was tracked from Google Scholar. Total citation of all tools is considered as 100% in each year and relative percentage of citations of each tool per year was calculated in relative to the total citations of all tools in the respective year.</p></caption><graphic xlink:href="gr1"></graphic></fig><table-wrap id="t0005" position="float"><label>Table 1</label><caption><p>Main online software tools for metagenomics studies</p></caption><table frame="hsides" rules="groups"><thead><tr><th><bold>Name</bold></th><th><bold>Weblink</bold></th><th><bold>Inbuilt annotation pipelines</bold></th><th><bold>Clustering methods</bold></th><th><bold>Online user support</bold></th><th><bold>Data storage</bold></th><th><bold>Rating</bold></th><th><bold>Refs.</bold></th></tr></thead><tbody><tr><td>MG-RAST</td><td><ext-link ext-link-type="uri" xlink:href="https://metagenomics.anl.gov/" id="ir005">https://metagenomics.anl.gov/</ext-link></td><td>SEED subsystem, COG, KO, NOG, eggNOG, M5RNA, KEGG, TrEMBL, SEED, PATRIC, SwissProt, GenBank, RefSeq</td><td>HM, PT, BC, T</td><td>Blog and manual</td><td>215,773 metagenome dataset and 30,589 public metagenomes</td><td><inline-graphic xlink:href="fx1.gif"></inline-graphic></td><td><xref rid="b0040" ref-type="bibr">[8]</xref>, <xref rid="b0055" ref-type="bibr">[11]</xref></td></tr><tr><td colspan="8">
</td></tr><tr><td>IMG/M</td><td><ext-link ext-link-type="uri" xlink:href="http://img.jgi.doe.gov/m" id="ir010">http://img.jgi.doe.gov/m</ext-link></td><td>COG, KOG, KEGG, KO, Pfam, TIGRfam, TIGR, MetaCyc, GO</td><td>T, PC, PT, RP, HM</td><td>User guide, user forum, standard operating procedure</td><td>32,802 genome and 5234 metagenome dataset</td><td><inline-graphic xlink:href="fx2.gif"></inline-graphic></td><td><xref rid="b0070" ref-type="bibr">[14]</xref>, <xref rid="b0075" ref-type="bibr">[15]</xref>, <xref rid="b0080" ref-type="bibr">[16]</xref>, <xref rid="b0085" ref-type="bibr">[17]</xref>, <xref rid="b0090" ref-type="bibr">[18]</xref></td></tr><tr><td colspan="8">
</td></tr><tr><td>METAREP</td><td><ext-link ext-link-type="uri" xlink:href="http://jcvi.org/metarep/" id="ir015">http://jcvi.org/metarep/</ext-link></td><td>GO, NCBI Taxonomy</td><td>T, HM, HCP</td><td>User manual, demo video</td><td>No storage</td><td><inline-graphic xlink:href="fx3.gif"></inline-graphic></td><td><xref rid="b0095" ref-type="bibr">[19]</xref>, <xref rid="b0100" ref-type="bibr">[20]</xref></td></tr><tr><td colspan="8">
</td></tr><tr><td>CoMet</td><td><ext-link ext-link-type="uri" xlink:href="http://comet.gobics.de/" id="ir020">http://comet.gobics.de/</ext-link></td><td>Pfam, GO</td><td>T, DG, BC, DM</td><td>Online help</td><td>No storage</td><td><inline-graphic xlink:href="fx4.gif"></inline-graphic></td><td><xref rid="b0105" ref-type="bibr">[21]</xref></td></tr><tr><td colspan="8">
</td></tr><tr><td>METAGENassist</td><td><ext-link ext-link-type="uri" xlink:href="http://www.metagenassist.ca/METAGENassist/" id="ir025">http://www.metagenassist.ca/METAGENassist/</ext-link></td><td>BacMap, GOLD, NCBI Taxonomy, PubMed</td><td>DG, HM, KM, SOM</td><td>Tutorials, FAQs, data examples</td><td>No storage</td><td><inline-graphic xlink:href="fx5.gif"></inline-graphic></td><td><xref rid="b0110" ref-type="bibr">[22]</xref></td></tr><tr><td colspan="8">
</td></tr><tr><td>MetaABC</td><td><ext-link ext-link-type="uri" xlink:href="http://metaabc.iis.sinica.edu.tw/" id="ir030">http://metaabc.iis.sinica.edu.tw/</ext-link></td><td>Database of reference genomes (NCBI)</td><td>HM, BC, PC</td><td>Online help</td><td>52 dataset</td><td><inline-graphic xlink:href="fx6.gif"></inline-graphic></td><td><xref rid="b0115" ref-type="bibr">[23]</xref></td></tr><tr><td colspan="8">
</td></tr><tr><td>MyTaxa</td><td><ext-link ext-link-type="uri" xlink:href="http://enve-omics.ce.gatech.edu/mytaxa/" id="ir035">http://enve-omics.ce.gatech.edu/mytaxa/</ext-link></td><td>Database of reference genes and genomes (NCBI)</td><td>PT, BC</td><td>FAQs, examples</td><td>No storage</td><td><inline-graphic xlink:href="fx7.gif"></inline-graphic></td><td><xref rid="b0120" ref-type="bibr">[24]</xref></td></tr><tr><td colspan="8">
</td></tr><tr><td>metaMicrobesOnline</td><td><ext-link ext-link-type="uri" xlink:href="http://meta.microbesonline.org/" id="ir040">http://meta.microbesonline.org/</ext-link></td><td>TIGRfam, COG, Pfam</td><td>T, PT</td><td>Guide, tutorial, help through email</td><td>155 metagenome and 3527 genome dataset</td><td><inline-graphic xlink:href="fx8.gif"></inline-graphic></td><td><xref rid="b0125" ref-type="bibr">[25]</xref>, <xref rid="b0130" ref-type="bibr">[26]</xref></td></tr><tr><td colspan="8">
</td></tr><tr><td>EBI Metagenomics</td><td><ext-link ext-link-type="uri" xlink:href="https://www.ebi.ac.uk/metagenomics/" id="ir045">https://www.ebi.ac.uk/metagenomics/</ext-link></td><td>RDP, Greengenes database, InterPro protein signature database</td><td>T, PC, BC, HM, SC, PCA</td><td>Training, online support by email and Twitter</td><td>141 projects and 5800 dataset</td><td><inline-graphic xlink:href="fx9.gif"></inline-graphic></td><td><xref rid="b0135" ref-type="bibr">[27]</xref></td></tr><tr><td colspan="8">
</td></tr><tr><td>CAMERA</td><td><ext-link ext-link-type="uri" xlink:href="http://camera.calit2.net/" id="ir050">http://camera.calit2.net/</ext-link></td><td>FragGeneScan, MetaGene, COG, Pfam, TIGRfam, GO, KEGG</td><td>T, PC, DG</td><td>Tutorials, video tutorials, online manual</td><td>128 projects and 2660 samples</td><td><inline-graphic xlink:href="fx10.gif"></inline-graphic></td><td><xref rid="b0140" ref-type="bibr">[28]</xref>, <xref rid="b0145" ref-type="bibr">[29]</xref></td></tr><tr><td colspan="8">
</td></tr><tr><td>METAVIR</td><td><ext-link ext-link-type="uri" xlink:href="http://metavir-meb.univ-bpclermont.fr/" id="ir055">http://metavir-meb.univ-bpclermont.fr/</ext-link></td><td>Pfam, RefSeq virus database</td><td>HM, DG, RP, PC</td><td>Video tutorial, guide, FAQs, online contact</td><td>170 viral metagenomic dataset and 335 projects</td><td><inline-graphic xlink:href="fx11.gif"></inline-graphic></td><td><xref rid="b0150" ref-type="bibr">[30]</xref>, <xref rid="b0155" ref-type="bibr">[31]</xref></td></tr><tr><td colspan="8">
</td></tr><tr><td>VIROME</td><td><ext-link ext-link-type="uri" xlink:href="http://virome.dbi.udel.edu/" id="ir060">http://virome.dbi.udel.edu/</ext-link></td><td>SEED, ACLAME, COG, GO, KEGG, MGOL, UniRef 100</td><td>T, PC, TDD</td><td>Tutorial videos</td><td>466 libraries containing 24,386,816 reads</td><td><inline-graphic xlink:href="fx12.gif"></inline-graphic></td><td><xref rid="b0160" ref-type="bibr">[32]</xref></td></tr></tbody></table><table-wrap-foot><fn><p><italic>Note:</italic> Darkness of the grayscale bars in the rating column indicates higher importance and usefulness. Rating is based on five different criteria represented with a gray scale from left to right: (i) easiness in data uploading, (ii) availability of online user support, (iii) spectrum of analysis, (iv) citation, and (v) stored data size. HM, heatmap; PT, phylogenetic tree; BC, bar chart; T, tabulation; PC, pie chart; RP, recruitment plot; HCP, hierarchical cluster plot; DM, distance matrix; DG, dendrogram; KM, K-means; SOM, self-organizing map; TDD, tab-delimited data; SC, stacked column; PCA, principal component analysis. Data storage was obtained from the respective website in October 2015.</p></fn></table-wrap-foot></table-wrap><table-wrap id="t0010" position="float"><label>Table 2</label><caption><p>Result of synthetic metagenome analysis using the five selected tools</p></caption><table frame="hsides" rules="groups"><thead><tr><th><bold>Tool</bold></th><th><bold>Total No. of microbial families identified</bold></th><th><bold>Analysis time course (h)</bold></th></tr></thead><tbody><tr><td>MG-RAST</td><td align="left">98</td><td align="char">05</td></tr><tr><td>IMG/M</td><td align="left">95</td><td align="char">96</td></tr><tr><td>EBI Metagenomics</td><td align="left">81</td><td align="char">04</td></tr><tr><td>CoMet</td><td align="left">172</td><td align="char">05</td></tr><tr><td>METAVIR</td><td align="left">100</td><td align="char">72</td></tr></tbody></table><table-wrap-foot><fn><p><italic>Note:</italic> Tools were selected based on rating criteria for taxonomic assessment using online support provided by the software developers.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc><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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