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An Integrative Method for Accurate Comparative Genome Mapping 英文参考文献
AnIntegrativeMethodforAccurate
ComparativeGenomeMapping
Firas Swidan1,2*,Eduardo P.C.Rocha3,4,Michael Shmoish1,Ron Y.Pinter1
1 Department of Computer Science, Technion, Israel Institute of Technology, Haifa, Israel, 2 Janelia Farm Research Center, Howard Hughes Medical Institute, Ashburn,
Virginia,UnitedStatesofAmerica,3AtelierdeBioinformatique,UniversityParisVI,Paris,France,4Unite′ GGB,InstitutPasteur,Paris,France
WepresentMAGIC,anintegrativeandaccuratemethodforcomparativegenomemapping.Ourmethodconsistsoftwo
phases: preprocessing for identifying ‘‘maximal similar segments,’’ and mapping for clustering and classifying these
segments. MAGIC’s main novelty lies in its biologically intuitive clustering approach, which aims towards both
calculating reorder-free segments and identifying orthologous segments. In the process, MAGIC efficiently handles
ambiguities resulting from duplications that occurred before the speciation of the considered organisms from their
mostrecentcommonancestor.WedemonstratebothMAGIC’srobustnessandscalability:theformerisassertedwith
respect to its initial input and with respect to its parameters’ values. The latter is asserted by applying MAGIC to
distantlyrelatedorganismsandtolargegenomes.WecompareMAGICtoothercomparativemappingmethodsand
provide detailed analysis of the differences between them. Our improvements allow a comprehensive study of the
diversity of genetic repertoires resulting from large-scale mutations, such as indels and duplications, including
explicitly transposable and phagic elements. The strength of our method is demonstrated by detailed statistics
computedforeachtypeoftheselarge-scalemutations.MAGICenabledustoconductacomprehensiveanalysisofthe
different forces shaping prokaryotic genomes from different clades, and to quantify the importance of novel gene
content introduced by horizontal gene transfer relative to gene duplication in bacterial genome evolution. We use
theseresultstoinvestigatethebreakpointdistribut
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