{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,3,29]],"date-time":"2022-03-29T08:29:38Z","timestamp":1648542578389},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"DOI":"10.13039\/501100004174","name":"Masdar Institute of Science and Technology","doi-asserted-by":"crossref","award":["SSG2015-000012"],"award-info":[{"award-number":["SSG2015-000012"]}],"id":[{"id":"10.13039\/501100004174","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1763-0","type":"journal-article","created":{"date-parts":[[2017,7,24]],"date-time":"2017-07-24T15:37:18Z","timestamp":1500910638000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture"],"prefix":"10.1186","volume":"18","author":[{"given":"Syafiq Kamarul","family":"Azman","sequence":"first","affiliation":[]},{"given":"Muhammad Zohaib","family":"Anwar","sequence":"additional","affiliation":[]},{"given":"Andreas","family":"Henschel","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,7,24]]},"reference":[{"issue":"6246","key":"1763_CR1","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1126\/science.aaa6882","volume":"349","author":"F Inagaki","year":"2015","unstructured":"Inagaki F, Hinrichs KU, Kubo Y, Bowles MW, Heuer VB, Hong WL, Hoshino T, Ijiri A, Imachi H, Ito M, Kaneko M, Lever MA, Lin YS, Meth\u00e9 B. A, Morita S, Morono Y, Tanikawa W, Bihan M, Bowden SA, Elvert M, Glombitza C, Gross D, Harrington GJ, Hori T, Li K, Limmer D, Liu CH, Murayama M, Ohkouchi N, Ono S, Park YS, Phillips SC, Prieto-Mollar X, Purkey M, Riedinger N, Sanada Y, Sauvage J, Snyder G, Susilawati R, Takano Y, Tasumi E, Terada T, Tomaru H, Trembath-Reichert E, Wang DT, Yamada Y. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor. Science. 2015; 349(6246):420\u20134. doi: 10.1126\/science.aaa6882 . Accessed 04 Mar 2017","journal-title":"Science"},{"issue":"7164","key":"1763_CR2","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1038\/nature06244","volume":"449","author":"PJ Turnbaugh","year":"2007","unstructured":"Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett C, Knight R, Gordon JI. The human microbiome project: exploring the microbial part of ourselves in a changing world. Nature. 2007; 449(7164):804.","journal-title":"Nature"},{"key":"1763_CR3","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s12915-014-0069-1","volume":"12","author":"JA Gilbert","year":"2014","unstructured":"Gilbert JA, Jansson JK, Knight R. The Earth Microbiome project: successes and aspirations. BMC Biology. 2014; 12:69. doi: 10.1186\/s12915-014-0069-1 . Accessed 04 Mar 2017","journal-title":"BMC Biology"},{"issue":"5","key":"1763_CR4","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nbt.1823","volume":"29","author":"P Yilmaz","year":"2011","unstructured":"Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PSG, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, Gil IS, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Meth\u00e9 BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spor A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Gl\u00f6ckner FO. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011; 29(5):415\u201320. doi: 10.1038\/nbt.1823 . Accessed 04 Mar 2017","journal-title":"Nat Biotechnol"},{"issue":"19","key":"1763_CR5","doi-asserted-by":"crossref","first-page":"2493","DOI":"10.1093\/bioinformatics\/bts470","volume":"28","author":"X Su","year":"2012","unstructured":"Su X, Xu J, Ning K. Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data. Bioinformatics. 2012; 28(19):2493\u2013501. doi: 10.1093\/bioinformatics\/bts470 . Accessed 04 Mar 2017","journal-title":"Bioinformatics"},{"issue":"1","key":"1763_CR6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/2047-217X-1-7","volume":"1","author":"D McDonald","year":"2012","unstructured":"McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, et al. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaScience. 2012; 1(1):1.","journal-title":"GigaScience"},{"key":"1763_CR7","first-page":"1019","volume":"39","author":"R Leinonen","year":"2010","unstructured":"Leinonen R, Sugawara H, Shumway M. The sequence read archive. Nucleic Acids Res. 2010; 39:1019.","journal-title":"Nucleic Acids Res"},{"key":"1763_CR8","doi-asserted-by":"crossref","unstructured":"Qiita. http:\/\/qiita.microbio.me . Accessed 16 Mar 2017.","DOI":"10.12968\/nuwa.2017.12.16"},{"issue":"1","key":"1763_CR9","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-15-41","volume":"15","author":"SM Huse","year":"2014","unstructured":"Huse SM, Welch DBM, Voorhis A, Shipunova A, Morrison HG, Eren AM, Sogin ML. VAMPS: a website for visualization and analysis of microbial population structures. BMC Bioinforma. 2014; 15(1):41.","journal-title":"BMC Bioinforma"},{"key":"1763_CR10","doi-asserted-by":"crossref","first-page":"037","DOI":"10.1093\/database\/baw037","volume":"2016","author":"DK Manter","year":"2016","unstructured":"Manter DK, Korsa M, Tebbe C, Delgado JA. myPhyloDB: a local web server for the storage and analysis of metagenomic data. Database. 2016; 2016:037.","journal-title":"Database"},{"issue":"23","key":"1763_CR11","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","volume":"75","author":"PD Schloss","year":"2009","unstructured":"Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al.Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75(23):7537\u201341.","journal-title":"Appl Environ Microbiol"},{"issue":"3","key":"1763_CR12","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1101\/gr.5969107","volume":"17","author":"DH Huson","year":"2007","unstructured":"Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007; 17(3):377\u201386.","journal-title":"Genome Res"},{"key":"1763_CR13","volume-title":"Proceedings of the 21th International Conference on Very Large Data Bases","author":"S Brin","year":"1995","unstructured":"Brin S. Near neighbor search in large metric spaces. In: Proceedings of the 21th International Conference on Very Large Data Bases. San Francisco: Morgan Kaufmann Publishers Inc.: 1995. http:\/\/dl.acm.org\/citation.cfm?id=673006 ."},{"issue":"1","key":"1763_CR14","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/0167-8655(94)90095-7","volume":"15","author":"ML Mic\u00f3","year":"1994","unstructured":"Mic\u00f3 ML, Oncina J, Vidal E. A new version of the nearest-neighbour approximating and eliminating search algorithm (aesa) with linear preprocessing time and memory requirements. Pattern Recogn Lett. 1994; 15(1):9\u201317.","journal-title":"Pattern Recogn Lett"},{"issue":"2","key":"1763_CR15","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1038\/ismej.2010.133","volume":"5","author":"C Lozupone","year":"2011","unstructured":"Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. Unifrac: an effective distance metric for microbial community comparison. ISME J. 2011; 5(2):169.","journal-title":"ISME J"},{"issue":"10","key":"1763_CR16","doi-asserted-by":"crossref","first-page":"1002743","DOI":"10.1371\/journal.pcbi.1002743","volume":"8","author":"SW Kembel","year":"2012","unstructured":"Kembel SW, Wu M, Eisen JA, Green JL. Incorporating 16s gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol. 2012; 8(10):1002743.","journal-title":"PLoS Comput Biol"},{"key":"1763_CR17","doi-asserted-by":"crossref","unstructured":"Ahmed M, Uddin MM, Azad MS, Haseeb S. Mysql performance analysis on a limited resource server: Fedora vs. ubuntu linux. In: Proceedings of the 2010 Spring Simulation Multiconference. San Diego: Society for Computer Simulation International: 2010. p. 99. http:\/\/dl.acm.org\/citation.cfm?id=1878641 .","DOI":"10.1145\/1878537.1878641"},{"issue":"10","key":"1763_CR18","doi-asserted-by":"crossref","first-page":"1004468","DOI":"10.1371\/journal.pcbi.1004468","volume":"11","author":"A Henschel","year":"2015","unstructured":"Henschel A, Anwar MZ, Manohar V. Comprehensive meta-analysis of ontology annotated 16S rRNA profiles identifies beta diversity clusters of environmental bacterial communities. PLoS Comput Biol. 2015; 11(10):1004468.","journal-title":"PLoS Comput Biol"},{"key":"1763_CR19","volume-title":"Distributed Computing with Python","author":"F Pierfederici","year":"2016","unstructured":"Pierfederici F. Distributed Computing with Python. Mumbai: Packt Publishing Ltd; 2016."},{"key":"1763_CR20","volume-title":"Redis in Action","author":"JL Carlson","year":"2013","unstructured":"Carlson JL. Redis in Action. Shelter Island: Manning Publications Co; 2013."},{"issue":"5","key":"1763_CR21","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","volume":"7","author":"JG Caporaso","year":"2010","unstructured":"Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al.Qiime allows analysis of high-throughput community sequencing data. Nat Methods. 2010; 7(5):335\u20136.","journal-title":"Nat Methods"},{"issue":"7","key":"1763_CR22","doi-asserted-by":"crossref","first-page":"5069","DOI":"10.1128\/AEM.03006-05","volume":"72","author":"TZ DeSantis","year":"2006","unstructured":"DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72(7):5069\u2013072.","journal-title":"Appl Environ Microbiol"},{"issue":"24","key":"1763_CR23","doi-asserted-by":"crossref","first-page":"3211","DOI":"10.1093\/bioinformatics\/bts611","volume":"28","author":"E Kopylova","year":"2012","unstructured":"Kopylova E, No\u00e9 L, Touzet H. Sortmerna: fast and accurate filtering of ribosomal rnas in metatranscriptomic data. Bioinformatics. 2012; 28(24):3211\u2013217.","journal-title":"Bioinformatics"},{"issue":"9","key":"1763_CR24","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1038\/nbt.2676","volume":"31","author":"MG Langille","year":"2013","unstructured":"Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R, et al.Predictive functional profiling of microbial communities using 16s rrna marker gene sequences. Nat Biotechnol. 2013; 31(9):814\u201321.","journal-title":"Nat Biotechnol"},{"key":"1763_CR25","doi-asserted-by":"crossref","unstructured":"Lagkouvardos I, Joseph D, Kapfhammer M, Giritli S, Horn M, Haller D, Clavel T. Imngs: A comprehensive open resource of processed 16s rrna microbial profiles for ecology and diversity studies. Sci Rep. 2016;6(33721). https:\/\/www.nature.com\/articles\/srep33721 .","DOI":"10.1038\/srep33721"},{"issue":"W1","key":"1763_CR26","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/nar\/gkt282","volume":"41","author":"GM Boratyn","year":"2013","unstructured":"Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, Madden TL, Matten WT, McGinnis SD, Merezhuk Y, et al.Blast: a more efficient report with usability improvements. Nucleic Acids Res. 2013; 41(W1):29\u201333.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"1763_CR27","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1109\/MCSE.2007.55","volume":"9","author":"JD Hunter","year":"2007","unstructured":"Hunter JD. Matplotlib: A 2d graphics environment. Comput Sci Eng. 2007; 9(3):90\u20135.","journal-title":"Comput Sci Eng"},{"issue":"12","key":"1763_CR28","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1109\/TVCG.2011.185","volume":"17","author":"M Bostock","year":"2011","unstructured":"Bostock M, Ogievetsky V, Heer J. D 3 data-driven documents. IEEE Trans Vis Comput Graph. 2011; 17(12):2301\u20139.","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"1763_CR29","unstructured":"mpld, 3: D3 Renderings of Matplotlib Graphics. https:\/\/github.com\/mpld3\/mpld3 . Accessed 16 Mar 2017."},{"issue":"3","key":"1763_CR30","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/0167-8655(86)90013-9","volume":"4","author":"EV Ruiz","year":"1986","unstructured":"Ruiz EV. An algorithm for finding nearest neighbours in (approximately) constant average time. Pattern Recogn Lett. 1986; 4(3):145\u201357.","journal-title":"Pattern Recogn Lett"},{"key":"1763_CR31","unstructured":"coord_util - Utility functions and modules for manipulating molecules for molecular dynamics simulations. https:\/\/github.com\/plediii\/coord_util . Accessed 12 Mar 2017."},{"key":"1763_CR32","doi-asserted-by":"crossref","DOI":"10.1007\/0-387-29151-2","volume-title":"Similarity Search: the Metric Space Approach vol. 32","author":"P Zezula","year":"2006","unstructured":"Zezula P, Amato G, Dohnal V, Batko M. Similarity Search: the Metric Space Approach vol. 32. New York: Springer; 2006."},{"key":"1763_CR33","doi-asserted-by":"crossref","unstructured":"McClelland J, Koslicki D. EMDUnifrac: Exact linear time computation of the Unifrac metric and identification of differentially abundant organisms. 2016. https:\/\/arxiv.org\/abs\/1611.04634 .","DOI":"10.1101\/087171"},{"issue":"12","key":"1763_CR34","doi-asserted-by":"crossref","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","volume":"71","author":"C Lozupone","year":"2005","unstructured":"Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005; 71(12):8228\u201335.","journal-title":"Appl Environ Microbiol"},{"key":"1763_CR35","doi-asserted-by":"crossref","unstructured":"Rocklin M. Dask: Parallel computation with blocked algorithms and task scheduling. In: Proceedings of the 14th Python in Science Conference. Austin: Citeseer: 2015. p. 130\u20136. http:\/\/conference.scipy.org\/proceedings\/scipy2015\/ .","DOI":"10.25080\/Majora-7b98e3ed-013"},{"issue":"1","key":"1763_CR36","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/2041-1480-4-43","volume":"4","author":"PL Buttigieg","year":"2013","unstructured":"Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE. The environment ontology: contextualising biological and biomedical entities. J Biomed Semant. 2013; 4(1):43.","journal-title":"J Biomed Semant"},{"key":"1763_CR37","doi-asserted-by":"crossref","first-page":"545","DOI":"10.7717\/peerj.545","volume":"2","author":"JR Rideout","year":"2014","unstructured":"Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, et al.Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ. 2014; 2:545.","journal-title":"PeerJ"},{"issue":"3","key":"1763_CR38","doi-asserted-by":"crossref","first-page":"89323","DOI":"10.1371\/journal.pone.0089323","volume":"9","author":"X Su","year":"2014","unstructured":"Su X, Pan W, Song B, Xu J, Ning K. Parallel-meta 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization. PLoS ONE. 2014; 9(3):89323.","journal-title":"PLoS ONE"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1763-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,13]],"date-time":"2020-10-13T08:06:36Z","timestamp":1602576396000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1763-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,7,24]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1763"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1763-0","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,7,24]]},"article-number":"353"}}