Species Choice for Comparative Genomics Being Greedy Works 英文参考文献.docVIP

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Species Choice for Comparative Genomics Being Greedy Works 英文参考文献.doc

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Species Choice for Comparative Genomics Being Greedy Works 英文参考文献

SpeciesChoiceforComparativeGenomics: BeingGreedyWorks Fabio Pardi*,Nick Goldman EMBL-EuropeanBioinformaticsInstitute,WellcomeTrustGenomeCampus,Hinxton,UnitedKingdom Several projects investigating genetic function and evolution through sequencing and comparison of multiple genomesarenowunderway.Theseprojectsconsumemanyresources,andappropriateplanningshouldbedevotedto choosingwhichspeciestosequence,potentiallyinvolvingcooperationamongdifferentsequencingcentres.Awidely discussedcriterionforspecieschoiceisthemaximisationofevolutionarydivergence.Ourmathematicalformalization ofthisproblemsurprisinglyshowsthatthebestlong-termcooperativestrategycoincideswiththeseeminglyshort- term‘‘greedy’’strategyofalwayschoosingthenextbestsinglespecies.Othercriteriainfluencingspecieschoice,such asmedicalrelevanceorsequencingcosts,canalsobeaccommodatedinourapproach,suggestingourresults’broad relevanceinscientificpolicydecisions. Citation:PardiF,GoldmanN(2005)Specieschoiceforcomparativegenomics:Beinggreedyworks.PLoSGenet1(6):e71. likelytoariseonlyfor(evolutionarily)verywidephylogenetic scopes,whichareunrealisticinpracticeduetotheresulting Introduction Comparing biological sequences has enormous potential forincreasingourknowledgeabouttheirfunction,structure, and evolution, an idea that has been applied virtually everywhere in computational biology. Comparative studies are now performed on a genomic scale, requiring the sequencing of entire genomes [1,2] or signi?cant parts of them [3]. Choosing the right species for sequencing is thereforecrucial.Thisinvolvestwodistinctdecisions:?rsta range of species over which comparisons will be made is identi?ed,andthenanumberofthemareselectedforactual sequencing.The?rstdecisionspeci?eswhatisknownasthe phylogeneticscope[4]orlinealscope[5]andismadelargely onthebasisofthebiologythespeciesarerequiredtoshare. Different research communities are focusing on different scopes—forexample,yeasts[6],nematodes[7],fruit?ies[8], mammals [9], and primates [10]—c