Long-Range Periodic Patterns in Microbial Genomes Indicate 长距离的微生物基因组中周期模式显示.ppt

Long-RangePeriodicPatternsinMicrobial

GenomesIndicateSignificantMulti-Scale

ChromosomalOrganization

(Allenet.al.,UCSD)presentedbySuvrajitMaji

BackgroundMaterials/MethodResultsDiscussionSummaryandConclusion

BackgroundGenesinbacterialnucleoidsarearrangedalongthelongaxisofthecell,topreservethelinearorderofthegenesalongthechromosome.Waveletanalysishasbeenusedtodetectsuchlong-rangeperiodicpatternsininherentlynoisychromosomeposition-dependentdataGeneorientationDNA-bendingprofiles,andgeneexpressiondatainprokaryotes,GC/ATskewoscillationsinhumanchromosomeswerestudied.

ApproachforDetectingGenomePosition-DependentPatterns

Materials/Method

Chromosomeposition-dependentdatawereanalyzedfor151prokaryoticorganisms(163chromosomesin16archaealand135bacterialorganisms):1)GC/ATcontentaveragedinkilobasebins,2)geneorientation(i.e.,strand),3)fractionalgenedensity(numberorfractionsofgenes—perkilobase),4)codonadaptationindex(CAI)pergene.CAImeasuresthetendencyofoneoftheavailablecodonstobepreferentiallyusedforcodingaspecificaminoacidresidue.

ThefilterfunctionusedinthisstudywastheMorletwavelet,definedasOrdereddata-f(x)x-nucleotidepositionalongthechromosome.g-familyoffilterfunctionsW-transformvaluea-filterwidths(scales)Scalogramistheplotofthesq.ofthemagnitudeoftransformvalue:

MoreonWavelets…Waveletanalysisisappliedtotimeseriesforwhichtraditionalmethods(e.gFourierTransform)appearunsatisfactory.Waveletanalysisdoesforunsteadyand/orintermittentsystemswhatFThasdoneformulti-periodicsystems.FThasnotimeresolution,notveryusefulonnon-stationarysignals.Localizationinbothtimeandfrequency

MoreonWavelets…complexwavelet,decomposedintwoparts:ThewaveletdefinedbyMorletis:

DescriptiveStatisticsforPatternStrengthsinGC/ATContent,GeneDensity,an