生物信息学课件

生物信息学课程内容1.

引言/分子生物学数据库2.

BLAST工具3.

EST拼接和电子克隆4.

序列对位排列5.

分子进化根底6.

分子系统发育分析方法7.

基因组分析8.

专题讲座〔6次〕9.开放讨论〔2次〕什么是生物信息学？Luscombe,N.M.etal.,2001.Whatisbioinformatics?MethodsofInformationinMedicine40:346-358.数据挖掘(DataMining)

关联Associating

分类Classifying

建模与模拟Modeling&Simulating

预测与检验Predicting&Testing发生在Wal*Mart的真实故事理念：相关联的货物最好摆在一起问题：啤酒和什么货物关联？可能的答案：花生米？红肠？……从上百万张收银单获得的答案：尿布！数据仓库(DataWarehouse)和数据挖掘(DataMining)数据挖掘流感的预测〔网上数据挖掘〕具体方法

AutomatedqueryselectionprocessComputationandpre-filteringConstructingtheILI-relatedqueryfractionFittingandvalidatingafinalmodelState-levelmodelvalidationBioinformatics〔CABIOS〕OxfordUniversityPressMPSS://.DomainInformation界面分子生物学数据库NCBINationalCenterforBiotechnologyInformation:///全球最大的生物信息资源中心DNA序列、蛋白质序列、出版物、数据挖掘工具等NCBI主页EMBnet北京大学生物信息学效劳器BioSino基因组信息资源GenBank(:///)DDBJ(:///)EMBL(/)DDBJEMBL(Germany)EMBL-EBI(UK)蛋白质信息资源PDB(:///)PIR(:///)SWISS－PROT(:///)TrEMBL(:///)NRL-3D(:///)密苏里植物园主页PDB密苏里植物园主页PIR密苏里植物园主页Swiss-Prot&TrEMBL密苏里植物园主页NRL-3DNARNucleicAcidsResearch(分子数据库专集)NucleicAcidsResearch(效劳器专集)Transposons:MobileGeneticElementsBarbaraMcClintockchromosomeTransposonGene基

因TransposonTransposonMutantGeneTaggedInsertionalMutagenesisTransgenesisTransposonEfficientTranspositionofpiggyBac(PB)TransposoninMiceAct-PBase+MammalianPBsystem(Dingetal.Cell2005)PB[RFP]PBaseMothpiggyBac(Caryetal.Virology1989)MorphologyMutantsWTMutantWT“Sandy”://,:///.INSERT界面

MP-PBmice

(insertionalmutationsmappingsystemofPBmice)ExperimentalProcedureFlowproductionAccess-controlTableExperimentalStageTableConstantTableStatusTableviewDetaildetailedinformationpagecommentboxInformationonrelationsbetweenmoleculesGenomesGenesPathwayOrthologsExpressionSequencesimilarityChemicalsandtheirreactionsKEGG数据库组织框架KEGG光合作用代谢通路rbcL基因及一个光合作用通路蛋白质相互作用数据库〔1〕蛋白质相互作用数据库〔2〕蛋白质相互作用数据库〔3〕蛋白质相互作用数据库〔4〕蛋白质相互作用数据库〔5〕其他数据库RatGenomeDatabase:///大鼠基因组相关数据专用工具(如VCMap–可视化比较作图软件)其他数据库UTRdb(非翻译区数据库):///有关3’和5’UTR信息主要的序列数据格式FASTAGenBankSwissProtASN.1XMLFASTA格式用于各种FASTA工具简要说明之后就是序列没有注释信息,只有序列例:>gi|1040960|gb|U35641.1|MMU35641MusmusculusBrca1mRNA,completecdsGGCACGAGGATCCAGCACCTCTCTTGGGGCTTCTCCGTCCTCGGCGCTTGGAAGTACGGATCTTTTTTCTCGGAGAAAAGTTCACTGGAACTGGAAGAAATGGATTTATCTGCCGTCCAAATTCAAGAAGTACAAAATGTCCTTCATGCTATGCAGAAAATCTTAGAGTGTCCGATCTGTTTGGAACTGATCAAAGAACCTGTTTCCACAAAGTGTGACCACATATTTTGCAAATTTTGTATGCTGAAACTTCTTAACCAGAAGAAAGGGCCTTCACAATGTCCTTTGTGTAAGAATGAGATAACCAAAAGGAGCCTACAGGGAAGCACAAGGTTTAGTCAGCTTGCTGAAGAGCTGCTGAGAATAATGGCTGCTTTTGAGCTTGACACGGGAATGCAGCTTACAAATGGTTTTAGTTTTTCAAAAAAGAGAAATAATTCTTGTGAGCGTTTGAATGAGGAGGCGTCGATCATCCAGAGCGTGGGCTACCGGAACCGTGTCAGAAGGCTTCCCCAGGTCGAACCTGGAAATGCCACCTTGAAGGACAGCCTAGGTGTCCAGCTGTCTAACCTTGGAATCGTGAGATCAGTGAAGAAAAACAGGCAGACCCAACCTCGAAAGAAATCTGTCTACATTGAACTAGACTCTGATTCTTCTGAAGAGACAGTAACTAAGCCAGGTGATTGCAGTGTGAGAGACC…

GenBank格式GenBank用纯文本文件注释、作者、版本等信息例:LOCUSMMU356415538bpmRNAlinearROD18-OCT-1996DEFINITIONMusmusculusBrca1mRNA,completecds.ACCESSIONU35641VERSIONU35641.1GI:1040960KEYWORDS.SOURCEhousemousestrain=C57Bl/6.ORGANISMMusmusculusEukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;Mammalia;Eutheria;Rodentia;Sciurognathi;Muridae;Murinae;Mus.REFERENCE1(bases1to5538)AUTHORSSharan,S.K.,Wims,M.andBradley,A.TITLEMurineBrca1:sequenceandsignificanceforhumanmissensemutationsJOURNALHum.Mol.Genet.4(12),2275-2278(1995)MEDLINE96177660PUBMED8634698SWISS-PROT格式用于SWISS-PROT数据库包括注释信息例:IDBRC1_MOUSESTANDARD;PRT;1812AA.ACP48754;Q60957;Q60983;DT01-FEB-1996(Rel.33,Created)DT01-NOV-1997(Rel.35,Lastsequenceupdate)DT16-OCT-2001(Rel.40,Lastannotationupdate)DEBreastcancertype1susceptibilityproteinhomolog.GNBRCA1.OSMusmusculus(Mouse).OCEukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;OCMammalia;Eutheria;Rodentia;Sciurognathi;Muridae;Murinae;Mus.OXNCBI_TaxID=10090;RN[1]RPSEQUENCEFROMN.A.RCSTRAIN=C57BL/6;TISSUE=Embryo;RXMEDLINE=96177659;PubMed=8634697;RAAbelK.J.,XyJ.,YinG.Y.,LyonsR.H.,MeislerM.H.,WeberB.L.;RT"MouseBrca1:localizationsequenceanalysisandidentificationofRTevolutionarilyconserveddomains.";RLHum.Mol.Genet.4:2265-2273(1995).…XML格式eXtensibleMarkupLanguage类似HTML国际标准半结构化例:<?xmlversion="1.0"?><!DOCTYPEGBSeqPUBLIC"-//NCBI//NCBIGBSeq/EN"“://"><GBSet><GBSeq><GBSeq_locus>MMU35641</GBSeq_locus><GBSeq_length>5538</GBSeq_length><GBSeq_strandednessvalue="not-set">0</GBSeq_strandedness><GBSeq_moltypevalue="mrna">5</GBSeq_moltype><GBSeq_topologyvalue="linear">1</GBSeq_topology><GBSeq_division>ROD</GBSeq_division><GBSeq_update-date>18-OCT-1996</GBSeq_update-date><GBSeq_create-date>25-OCT-1995</GBSeq_create-date><GBSeq_definition>MusmusculusBrca1mRNA,completecds</GBSeq_definition><GBSeq_primary-accession>U35641</GBSeq_primary-accession><GBSeq_accession-version>U35641.1</GBSeq_accession-version>ASN.1格式国际标准半结构化格式用于NCBI数据例:Seq-entry::=set{level1,classnuc-prot,descr{title"MusmusculusBrca1mRNA,andtranslatedproducts",source{org{taxname"Musmusculus",db{{db"taxon",tagid10090}},orgname{namebinomial{genus"Mus"