Algebraic Distribution of Segmental Duplication Lengths in Whole-Genome Sequence Self-Alignments 英文参考文献.docVIP
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Algebraic Distribution of Segmental Duplication Lengths in Whole-Genome Sequence Self-Alignments 英文参考文献
AlgebraicDistributionofSegmentalDuplicationLengths
inWhole-GenomeSequenceSelf-Alignments
KunGao,JonathanMiller*
PhysicsandBiologyUnit,OkinawaInstituteofScienceandTechnology,Kunigami,Okinawa,Japan
Abstract
Distributions of duplicated sequences from genome self-alignment are characterized, including forward and backward
alignments in bacteria and eukaryotes. A Markovian process without auto-correlation should generate an exponential
distribution expected from local effects of point mutation and selection on localised function; however, the observed
distributionsshowsubstantialdeviationfromexponentialform–theyareroughlyalgebraicinstead–suggestinganovel
kindoflong-distancecorrelationthatmustbenon-localinorigin.
Citation:GaoK,MillerJ(2011)AlgebraicDistributionofSegmentalDuplicationLengthsinWhole-GenomeSequenceSelf-Alignments.PLoSONE6(7):e18464.
doi:10.1371/journal.pone.0018464
Editor:RobertDeSalle,AmericanMuseumofNaturalHistory,UnitedStatesofAmerica
ReceivedSeptember17,2010;AcceptedMarch8,2011;PublishedJuly14,2011
Copyright: ? 2011 Gao, Miller. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited.
Funding:Theauthorshavenosupportorfundingtoreport.
CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexist.
*E-mail:jm@oist.jp
Introduction
almostacentury.Thus,Baileyetal.observedin2002thatrecent
SD,definedassequencepairslongerthan1kb(kilobase)withat
least90%identity,accountforsome5%ofthehumangenome[6]
andareofteninvolvedinchromosomerearrangementsunderlying
geneticdisease.SubsequentlyCputedthataround
3:5%oftheapproximately3gigabasehumangenomeconsistsof
SD,definedasatleasttwosequenceslongerthan5kbandsharing
morethan90%identity.PatternsofSDwerefurthercharacterized
byZhangetal.[7].
The basic mechanisms of genome sequence evolution include
point mutation, insertion and deletion, and recombination; in
p
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