MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
Identifieur interne : 000491 ( Main/Exploration ); précédent : 000490; suivant : 000492MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
Auteurs : Jens Roat Kultima [Allemagne] ; Shinichi Sunagawa [Allemagne] ; Junhua Li [République populaire de Chine] ; Weineng Chen [République populaire de Chine] ; Hua Chen [République populaire de Chine] ; Daniel R. Mende [Allemagne] ; Manimozhiyan Arumugam [Allemagne] ; Qi Pan [République populaire de Chine] ; Binghang Liu [République populaire de Chine] ; Junjie Qin [République populaire de Chine] ; Jun Wang [République populaire de Chine] ; Peer Bork [Allemagne]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at
Url:
DOI: 10.1371/journal.pone.0047656
PubMed: 23082188
PubMed Central: 3474746
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000611
- to stream Pmc, to step Curation: 000611
- to stream Pmc, to step Checkpoint: 000402
- to stream Ncbi, to step Merge: 000364
- to stream Ncbi, to step Curation: 000364
- to stream Ncbi, to step Checkpoint: 000364
- to stream Main, to step Merge: 000492
- to stream Main, to step Curation: 000491
Le document en format XML
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Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Pan, Qi" sort="Pan, Qi" uniqKey="Pan Q" first="Qi" last="Pan">Qi Pan</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Binghang" sort="Liu, Binghang" uniqKey="Liu B" first="Binghang" last="Liu">Binghang Liu</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Qin, Junjie" sort="Qin, Junjie" uniqKey="Qin J" first="Junjie" last="Qin">Junjie Qin</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of 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type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Sunagawa, Shinichi" sort="Sunagawa, Shinichi" uniqKey="Sunagawa S" first="Shinichi" last="Sunagawa">Shinichi Sunagawa</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Li, Junhua" sort="Li, Junhua" uniqKey="Li J" first="Junhua" last="Li">Junhua Li</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, Guangdong, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Weineng" sort="Chen, Weineng" uniqKey="Chen W" first="Weineng" last="Chen">Weineng Chen</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Hua" sort="Chen, Hua" uniqKey="Chen H" first="Hua" last="Chen">Hua Chen</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Mende, Daniel R" sort="Mende, Daniel R" uniqKey="Mende D" first="Daniel R." last="Mende">Daniel R. Mende</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Arumugam, Manimozhiyan" sort="Arumugam, Manimozhiyan" uniqKey="Arumugam M" first="Manimozhiyan" last="Arumugam">Manimozhiyan Arumugam</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Pan, Qi" sort="Pan, Qi" uniqKey="Pan Q" first="Qi" last="Pan">Qi Pan</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Binghang" sort="Liu, Binghang" uniqKey="Liu B" first="Binghang" last="Liu">Binghang Liu</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Qin, Junjie" sort="Qin, Junjie" uniqKey="Qin J" first="Junjie" last="Qin">Junjie Qin</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Science and Technology, BGI-Shenzhen, Shenzhen, Guangdong</wicri:regionArea><wicri:noRegion>Guangdong</wicri:noRegion></affiliation></author><author><name sortKey="Bork, Peer" sort="Bork, Peer" uniqKey="Bork P" first="Peer" last="Bork">Peer Bork</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Max-Delbruck-Centre for Molecular Medicine, Berlin-Buch, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Delbruck-Centre for Molecular Medicine, Berlin-Buch</wicri:regionArea><wicri:noRegion>Berlin-Buch</wicri:noRegion><wicri:noRegion>Berlin-Buch</wicri:noRegion><wicri:noRegion>Berlin-Buch</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at <ext-link ext-link-type="uri" xlink:href="http://www.bork.embl.de/mocat/">http://www.bork.embl.de/mocat/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Goecks, J" uniqKey="Goecks J">J Goecks</name></author><author><name sortKey="Nekrutenko, A" uniqKey="Nekrutenko A">A Nekrutenko</name></author><author><name sortKey="Taylor, J" uniqKey="Taylor J">J Taylor</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, Em" uniqKey="Glass E">EM Glass</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></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Markowitz, Vm" uniqKey="Markowitz V">VM Markowitz</name></author><author><name sortKey="Chen, I Ma" uniqKey="Chen I">I-MA 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></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Angiuoli, Sv" uniqKey="Angiuoli S">SV Angiuoli</name></author><author><name sortKey="Matalka, M" uniqKey="Matalka M">M Matalka</name></author><author><name sortKey="Gussman, A" uniqKey="Gussman A">A Gussman</name></author><author><name sortKey="Galens, K" uniqKey="Galens K">K Galens</name></author><author><name sortKey="Vangala, M" uniqKey="Vangala M">M Vangala</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Arumugam, M" uniqKey="Arumugam M">M Arumugam</name></author><author><name sortKey="Harrington, Ed" uniqKey="Harrington E">ED Harrington</name></author><author><name sortKey="Foerstner, Ku" uniqKey="Foerstner K">KU Foerstner</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="Huson, Dh" uniqKey="Huson D">DH Huson</name></author><author><name sortKey="Mitra, S" uniqKey="Mitra S">S Mitra</name></author><author><name sortKey="Ruscheweyh, H J" uniqKey="Ruscheweyh H">H-J Ruscheweyh</name></author><author><name sortKey="Weber, N" uniqKey="Weber N">N Weber</name></author><author><name sortKey="Schuster, Sc" uniqKey="Schuster S">SC Schuster</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qin, J" uniqKey="Qin J">J Qin</name></author><author><name sortKey="Li, R" uniqKey="Li R">R Li</name></author><author><name sortKey="Raes, J" uniqKey="Raes J">J Raes</name></author><author><name sortKey="Arumugam, M" uniqKey="Arumugam M">M Arumugam</name></author><author><name sortKey="Burgdorf, Ks" uniqKey="Burgdorf K">KS Burgdorf</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peterson, J" uniqKey="Peterson J">J Peterson</name></author><author><name sortKey="Garges, S" uniqKey="Garges S">S Garges</name></author><author><name sortKey="Giovanni, M" uniqKey="Giovanni M">M Giovanni</name></author><author><name sortKey="Mcinnes, P" uniqKey="Mcinnes P">P McInnes</name></author><author><name sortKey="Wang, L" uniqKey="Wang L">L Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gilbert, Ja" uniqKey="Gilbert J">JA Gilbert</name></author><author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name></author><author><name sortKey="Antonopoulos, D" uniqKey="Antonopoulos D">D Antonopoulos</name></author><author><name sortKey="Balaji, P" uniqKey="Balaji P">P Balaji</name></author><author><name sortKey="Brown, Ct" uniqKey="Brown C">CT Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simpson, Da" uniqKey="Simpson D">DA Simpson</name></author><author><name sortKey="Clark, Gr" uniqKey="Clark G">GR Clark</name></author><author><name sortKey="Alexander, S" uniqKey="Alexander S">S Alexander</name></author><author><name sortKey="Silvestri, G" uniqKey="Silvestri G">G Silvestri</name></author><author><name sortKey="Willoughby, Ce" uniqKey="Willoughby C">CE Willoughby</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gonzalez, A" uniqKey="Gonzalez A">A Gonzalez</name></author><author><name sortKey="Knight, R" uniqKey="Knight R">R Knight</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mende, Dr" uniqKey="Mende D">DR Mende</name></author><author><name sortKey="Waller, As" uniqKey="Waller A">AS Waller</name></author><author><name sortKey="Sunagawa, S" uniqKey="Sunagawa S">S Sunagawa</name></author><author><name sortKey="J Rvelin, Ai" uniqKey="J Rvelin A">AI Järvelin</name></author><author><name sortKey="Chan, Mm" uniqKey="Chan M">MM Chan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cox, Mp" uniqKey="Cox M">MP Cox</name></author><author><name sortKey="Peterson, Da" uniqKey="Peterson D">DA Peterson</name></author><author><name sortKey="Biggs, Pj" uniqKey="Biggs P">PJ Biggs</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schwartz, S" uniqKey="Schwartz S">S Schwartz</name></author><author><name sortKey="Oren, R" uniqKey="Oren R">R Oren</name></author><author><name sortKey="Ast, G" uniqKey="Ast G">G Ast</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, R" uniqKey="Li R">R Li</name></author><author><name sortKey="Yu, C" uniqKey="Yu C">C Yu</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Lam, T W" uniqKey="Lam T">T-W Lam</name></author><author><name sortKey="Yiu, S M" uniqKey="Yiu S">S-M Yiu</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Haas, Bj" uniqKey="Haas B">BJ Haas</name></author><author><name sortKey="Gevers, D" uniqKey="Gevers D">D Gevers</name></author><author><name sortKey="Earl, Am" uniqKey="Earl A">AM Earl</name></author><author><name sortKey="Feldgarden, M" uniqKey="Feldgarden M">M Feldgarden</name></author><author><name sortKey="Ward, Dv" uniqKey="Ward D">DV Ward</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></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ciccarelli, Fd" uniqKey="Ciccarelli F">FD Ciccarelli</name></author><author><name sortKey="Doerks, T" uniqKey="Doerks T">T Doerks</name></author><author><name sortKey="Von Mering, C" uniqKey="Von Mering C">C von Mering</name></author><author><name sortKey="Creevey, Cj" uniqKey="Creevey C">CJ Creevey</name></author><author><name sortKey="Snel, B" uniqKey="Snel B">B Snel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hyatt, D" uniqKey="Hyatt D">D Hyatt</name></author><author><name sortKey="Chen, G L" uniqKey="Chen G">G-L Chen</name></author><author><name sortKey="Locascio, Pf" uniqKey="Locascio P">PF Locascio</name></author><author><name sortKey="Land, Ml" uniqKey="Land M">ML Land</name></author><author><name sortKey="Larimer, Fw" uniqKey="Larimer F">FW Larimer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhu, W" uniqKey="Zhu W">W Zhu</name></author><author><name sortKey="Lomsadze, A" uniqKey="Lomsadze A">A Lomsadze</name></author><author><name sortKey="Borodovsky, M" uniqKey="Borodovsky M">M Borodovsky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Karsenti, E" uniqKey="Karsenti E">E Karsenti</name></author><author><name sortKey="Acinas, Sg" uniqKey="Acinas S">SG Acinas</name></author><author><name sortKey="Bork, P" uniqKey="Bork P">P Bork</name></author><author><name sortKey="Bowler, C" uniqKey="Bowler C">C Bowler</name></author><author><name sortKey="De Vargas, C" uniqKey="De Vargas C">C De Vargas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cock, Pja" uniqKey="Cock P">PJA Cock</name></author><author><name sortKey="Fields, Cj" uniqKey="Fields C">CJ Fields</name></author><author><name sortKey="Goto, N" uniqKey="Goto N">N Goto</name></author><author><name sortKey="Heuer, Ml" uniqKey="Heuer M">ML Heuer</name></author><author><name sortKey="Rice, Pm" uniqKey="Rice P">PM Rice</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>République populaire de Chine</li></country><region><li>Bade-Wurtemberg</li><li>District de Karlsruhe</li></region><settlement><li>Heidelberg</li></settlement></list><tree><country name="Allemagne"><region name="Bade-Wurtemberg"><name sortKey="Kultima, Jens Roat" sort="Kultima, Jens Roat" uniqKey="Kultima J" first="Jens Roat" last="Kultima">Jens Roat Kultima</name></region><name sortKey="Arumugam, Manimozhiyan" sort="Arumugam, Manimozhiyan" uniqKey="Arumugam M" first="Manimozhiyan" last="Arumugam">Manimozhiyan Arumugam</name><name sortKey="Bork, Peer" sort="Bork, Peer" uniqKey="Bork P" first="Peer" last="Bork">Peer Bork</name><name sortKey="Bork, Peer" sort="Bork, Peer" uniqKey="Bork P" first="Peer" last="Bork">Peer Bork</name><name sortKey="Mende, Daniel R" sort="Mende, Daniel R" uniqKey="Mende D" first="Daniel R." last="Mende">Daniel R. Mende</name><name sortKey="Sunagawa, Shinichi" sort="Sunagawa, Shinichi" uniqKey="Sunagawa S" first="Shinichi" last="Sunagawa">Shinichi Sunagawa</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Li, Junhua" sort="Li, Junhua" uniqKey="Li J" first="Junhua" last="Li">Junhua Li</name></noRegion><name sortKey="Chen, Hua" sort="Chen, Hua" uniqKey="Chen H" first="Hua" last="Chen">Hua Chen</name><name sortKey="Chen, Weineng" sort="Chen, Weineng" uniqKey="Chen W" first="Weineng" last="Chen">Weineng Chen</name><name sortKey="Li, Junhua" sort="Li, Junhua" uniqKey="Li J" first="Junhua" last="Li">Junhua Li</name><name sortKey="Liu, Binghang" sort="Liu, Binghang" uniqKey="Liu B" first="Binghang" last="Liu">Binghang Liu</name><name sortKey="Pan, Qi" sort="Pan, Qi" uniqKey="Pan Q" first="Qi" last="Pan">Qi Pan</name><name sortKey="Qin, Junjie" sort="Qin, Junjie" uniqKey="Qin J" first="Junjie" last="Qin">Junjie Qin</name><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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