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Barcode Server A Visualization-Based Genome Analysis System.doc

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Barcode Server A Visualization-Based Genome Analysis System

BarcodeServer:AVisualization-BasedGenomeAnalysis System FenglouMao1,2,VictorOlman1,YanWang3,YingXu1,2,3* 1ComputationalSystemsBiologyLab,DepartmentofBiochemistryandMolecularBiologyandInstituteofBioinformatics,UniversityofGeorgia,Athens,Georgia,United StatesofAmerica,2BioEnergyScienceCenter(BESC),UniversityofGeorgia,Athens,Georgia,UnitedStatesofAmerica,3CollegeofComputerScienceandTechnology, JilinUniversity,Changchun,China Abstract We have previously developed a computational method for representing a genome as a barcode image, which makes variousgenomicfeaturesvisuallyapparent.Wehavedemonstratedthatthisvisualcapabilityhasmadesomechallenging genomeanalysisproblemsrelativelyeasytosolve.Wehaveappliedthiscapabilitytoanumberofchallengingproblems, including(a)identificationofhorizontallytransferredgenes,(b)identificationofgenomicislandswithspecialpropertiesand (c)binningofmetagenomicsequences,andachievedhighlyencouragingresults.Theseapplicationresultsinspiredusto develop this barcode-based genome analysis server for public service, which supports the following capabilities: (a) calculationofthek-merbasedbarcodeimageforaprovidedDNAsequence;(b)detectionofsequencefragmentsinagiven genomewithdistinctbarcodesfromthoseofthemajorityofthegenome,(c)clusteringofprovidedDNAsequencesinto groupshavingsimilarbarcodes;and(d)homology-basedsearchusingBlastagainstagenomedatabaseforanyselected genomicregionsdeemedtohaveinterestingbarcodes.Thebarcodeserverprovidesajobmanagementcapability,allowing processing of a large number of analysis jobs for barcode-based comparative genome analyses. The barcode server is accessibleat/Barcode. Citation: Mao F, Olman V, Wang Y, Xu Y (2013) Barcode Server: A Visualization-Based Genome Analysis System. PLoS ONE 8(2): e56726. doi:10.1371/ journal.pone.0056726 Editor:Shu-DongZhang,Queen’sUniversityBelfast,UnitedKingdom ReceivedOctober10,2012;AcceptedJanuary14,2013;PublishedFebruary15,2013 Thisisanopen-accessarticle,freeofallcopyright,andmaybefreelyreproduced,