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LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa

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dc.contributor.authorTian, Longen
dc.contributor.authorHuang, Chengjieen
dc.contributor.authorMazloom, Rezaen
dc.contributor.authorHeath, Lenwood S.en
dc.contributor.authorVinatzer, Boris A.en
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2020-07-16T18:35:44Zen
dc.date.available2020-07-16T18:35:44Zen
dc.date.issued2020-03-30en
dc.description.abstractHigh throughput DNA sequencing in combination with efficient algorithms could provide the basis for a highly resolved, genome phylogeny-based and digital prokaryotic taxonomy. However, current taxonomic practice continues to rely on cumbersome journal publications for the description of new species, which still constitute the smallest taxonomic units. In response, we introduce LINbase, a web server that allows users to genomically circumscribe any group of prokaryotes with measurable DNA similarity and that uses the individual isolate as smallest unit. Since LINbase leverages the concept of Life Identification Numbers (LINs), which are codes assigned to individual genomes based on reciprocal average nucleotide identity, we refer to groups circumscribed in LINbase as LINgroups. Users can associate with each LINgroup a name, a short description, and a URL to a peer-reviewed publication. As soon as a LINgroup is circumscribed, any user can immediately identify query genomes as members and submit comments about the LINgroup. Most genomes currently in LINbase were imported from GenBank, but users can upload their own genome sequences as well. In conclusion, LINbase combines the resolution of LINs with the power of crowdsourcing in support of a highly resolved, genome phylogeny-based digital taxonomy. LINbase is available at http://www.LINbase.org.en
dc.description.sponsorshipNational Science Foundation [IOS-1354215, in part]; College of Agriculture and Life Sciences, Virginia Polytechnic Institute and State University; Virginia Agricultural Experiment Station (to B.A.V.) (in part); Hatch Program of the National Institute of Food and Agriculture, US Department of Agriculture (to B.A.V.). Funding for open access charge: National Science Foundation; Institutional Funds.en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gkaa190en
dc.identifier.urihttp://hdl.handle.net/10919/99364en
dc.identifier.volume48en
dc.language.isoenen
dc.publisherOxford University Pressen
dc.rightsCreative Commons Attribution-NonCommercial 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/en
dc.titleLINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxaen
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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