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dc.date.accessioned2017-08-08T10:00:09Z
dc.date.available2017-08-08T10:00:09Z
dc.date.created2013-08-22T11:04:13Z
dc.date.issued2013
dc.identifier.citationVesth, Tammi Lagesen, Karin Acar, Öncel Ussery, David . CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics. PLoS ONE. 2013, 8(4), 1-16
dc.identifier.urihttp://hdl.handle.net/10852/56843
dc.description.abstractBackground: Today, there are more than a hundred times as many sequenced prokaryotic genomes than were present in the year 2000. The economical sequencing of genomic DNA has facilitated a whole new approach to microbial genomics. The real power of genomics is manifested through comparative genomics that can reveal strain specific characteristics, diversity within species and many other aspects. However, comparative genomics is a field not easily entered into by scientists with few computational skills. The CMG-biotools package is designed for microbiologists with limited knowledge of computational analysis and can be used to perform a number of analyses and comparisons of genomic data. Results: The CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the system alongside any other operating system. Source codes for all programs are provided under GNU license, which makes it possible to transfer the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing the diversity within the class Negativicutes, represented by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures. Conclusion: This paper shows the strength and diverse use of the CMG-biotools system. The system can be installed on a vide range of host operating systems and utilizes as much of the host computer as desired. It allows the user to compare multiple genomes, from various sources using standardized data formats and intuitive visualizations of results. The examples presented here clearly shows that users with limited computational experience can perform complicated analysis without much training.en_US
dc.languageEN
dc.publisherPublic Library of Science (PLoS)
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleCMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomicsen_US
dc.typeJournal articleen_US
dc.creator.authorVesth, Tammi
dc.creator.authorLagesen, Karin
dc.creator.authorAcar, Öncel
dc.creator.authorUssery, David
cristin.unitcode185,15,29,50
cristin.unitnameCentre for Ecological and Evolutionary Synthesis
cristin.ispublishedtrue
cristin.fulltextoriginal
cristin.fulltextoriginal
cristin.qualitycode1
dc.identifier.cristin1044574
dc.identifier.bibliographiccitationinfo:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PLoS ONE&rft.volume=8&rft.spage=1&rft.date=2013
dc.identifier.jtitlePLoS ONE
dc.identifier.volume8
dc.identifier.issue4
dc.identifier.startpage1
dc.identifier.endpage16
dc.identifier.doihttp://dx.doi.org/10.1371/journal.pone.0060120
dc.identifier.urnURN:NBN:no-59666
dc.type.documentTidsskriftartikkelen_US
dc.type.peerreviewedPeer reviewed
dc.source.issn1932-6203
dc.identifier.fulltextFulltext https://www.duo.uio.no/bitstream/handle/10852/56843/2/journal-pone-0060120%25281%2529.pdf
dc.type.versionPublishedVersion
cristin.articleide60120


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