直系同源基因的识别方法与数据库

,,.,.,.:orthology,,,WalterFitch1970;paralogy,,[1,2].1,:2012-12-10;:2013-01-10:31172076;30970346:(1988-),,,,;*:1962-,,,,,,Tel:[phone],E-mail:[e-mail].杨婧,黄原*,汪晓阳,710062:直系同源（orthology）是指由于物种形成事件而享有共同祖先的基因之间的关系,直系同源基因之间通常具有相似的结构和生物学功能.由于基因组和转录组序列的快速积累,精确的识别直系同源基因有助于功能基因的注释,比较和进化基因组学研究.综述了现有的识别直系同源基因的主要方法,并列举了由此构建的数据库.这些方法可以归纳为三大类,第一类是基于序列相似性的方法,具有识别速度快以及灵敏度高等优点；第二类是基于构建系统发育树的方法,具有准确性高和信息量大等优点;第三类是将上述两种方法结合起来的混合方法,更好地平衡了灵敏性和准确性.最后总结了识别过程所面临的问题.:直系同源;直系同源识别;数据库:Q953:A:1007-7847（2013）03-0274-04MethodsandDatabasesforIdentificationofOrthologsYANGJing,HUANGYuan*,WANGXiao-yang(CollegeofLifeSciences,ShaanxiNormalUniversity,Xi′an710062,Shaanxi,China)AbstractOrthologousgenesarethosederivedfromacommonancestorthroughspeciation,andtypicallyre-tainsimilararchitectureandbiologicalfunction.Becauseofrapidaccumulationofgenomicandtranscrip-tomicsequence,automatedidentificationoforthologycanfacilitatefunctionalannotation,andstudiesoncomparativeandevolutionarygenomics.Themainmethodsoforthologspredictionandcorrespondingdatabasesconstructedwiththesemethodswerebrieflyreviewedhere.Thesemethodscanbegroupedintothreekinds,thefirstissimilarity-basedmethod,ithashighsensibilityandfastspeed;thesecondistree-basedmethod,itispreciseandinformative;thethirdishybridmethod,itistheoptimaltrade-offbetweenprecisionandsensibility.Finallytheproblemsfacedbytherecognitionprocessweresummarized.Keywords:orthology;orthologidentification;databaseLifeScienceResearch2013173274～277··173生命科学研究Vol．17No．320136LifeScienceResearchJun.20133,[3],,,、[4].,,.、、、,、、.,,.,,[5].、.,,.,.[6],[7].,,.2,,,.:,.:;;.2.1,.,[8].1.,[9].,,,,.2.2.,,,.,,,[17],.2.、,[18].:,,,;,;,;,,,,[19].2.3,.En-semblCompara;OPM(OrthoParaMap)PhyOP(Phylogeneticorthologyandparalogy)[25],Orthoin-spector[26].,,,.3,27520131Table1MethodsanddatabasesbasedonsequencesimilarityforidentificationoforthologsResourcesCOGclustersoforthologousgroupseggNOG(evolutionarygenealogyofgenes:non-supervisedorthologousgroups)OrthoMCL-DBInparanoid/multiparanoidOMA(orthologousmatrix)RoundUpOrthoDBthehierarchicalcatalogoforthologsMSOAROrthoSelectP-POD(princetonproteinorthologydatabase)BLASTOProteinorthoQuartetS-DBMethodsandtraits630.1133.MarkovOrthoMCL-DBversion5150.in-paralogsout-paralogs7.099[10].1320.reciprocalsmallestdistanceRSD)31807.GOInterPro48、33、7312[11].[8].ESTscDNA[12].[13].NCBICOG、EOG、OrthoMCL,MultiParanoidTIGREGO[14].NCBI717[15].QuartetS1621136592164[16].Websites://eggnog.embl.de://InParanoid.sbc.su.se://cegg.unige.ch/orthodb://ortholog.princeton.edu://://applications.bioanalysis.org/quartetsdb2Table2MethodsanddatabasesbasedontreesforidentificationoforthologsResourcesTreeFamLOFT(levelsoforthologyfromtrees)RIO(resampledinferenceoforthologs)PhylomeDBHCOPHGNCcomparisonoforthologypredictionsPHOG(phyloFactsorthologygroup)OrthologIDMethodsandtraits254..SDIspeciationduplicationinference[20].、[21].、、[22].PhyloFacts-per-orthologs.[23,24].Websites://rio.janelia.org/://phylogenomics.berkeley.edu/phog/[27].,;、、[28],;,..,.,,,.,、.（References）:[1]SONNHAMMEREL,KOONINEV.Orthology,paralogyandproposedclassificationforparalogsubtypes[J].TrendsinGe-netics,2002,18(12):619-620.[2]GABALD魷NT,DESSIMOZC,HUXLEY-JONESJ,etal.Join-ingforcesinthequestfororthologs[J].GenomeBiology,2009,10(9):403.[3]CHENF,MACKEYAJ,VERMUNTJK,etal.Assessingper-formanceoforthologydetectionstrategiesappliedtoeukaryoticgenomes[J].PLoSOne,2007,2(4):e383.[4],,,.[J].PANZeng-xiang,XUDan,ZHANGJin-bi,etal.Reviewsincomparativegenomicresearchbasedonor-thologs[J].Hereditas,2009,31(5):457-463.[5]CONTEMG,GAILLARDS,DROCG,etal.Phylogenomicsofplantgenomes:amethodologyforgenome-widesearchesforor-thologsinplants[J].BMCGenomics,2008,(9):183.[6]ALTENHOFFAM,DESSIMOZC.Phylogeneticandfunctionalassessmentoforthologsinferenceprojectsandmethods[J].PLoSComputationalBiology,2009,5(1):e1000262.[7]SENNBLANDB,LAGERGRENJ.Probabilisticorthologyanal-ysis[J].SystemBiology,2009,58(4):411-424.[8]SHIG,PENGMC,JIANGT.MultiMSOAR2.0:anaccuratetooltoidentifyorthologgroupsamongmultiplegenomes[J].PLoSOne,2011,6(6):e20892.[9]TRACHANAK,LARSSONTA,POWELLLS,etal.Ortholo-gypredictionmethods:aqualityassessmentusingcruatedpro-teinfamilies[J].Bioessays,2011,33(10):769-780.[10]魶STLUNDG,SCHMITTT,FORSLUNDK,etal.InParanoid7:newalgorithmsandtoolsforeukaryoticorthologyanalysis[J].NucleicAcidsResearch,2010,38(suppl1):196-203.[11]WATERHOUSERM,ZDOBNOVEM,TEGENFELDTF,etal.OrthoDB:thehierarchicalcatalogofeukaryoticorthologsin2011[J].NucleicAcidsResearch,2011,39(suppl1):283-288.[12]SCHREIBERF,PICKK,ERPENBECKD,etal.OrthoSelect:aprotocolforselectingorthologousgroupsinphylogenomics[J].BMCBioinformatics,2009,(10