生物信息學(xué)課件

生物信息學(xué)課程內(nèi)容1.

引言/分子生物學(xué)數(shù)據(jù)庫(kù)2.

BLAST工具3.

EST拼接和電子克隆4.

序列對(duì)位排列5.

分子進(jìn)化根底6.

分子系統(tǒng)發(fā)育分析方法7.

基因組分析8.

專題講座〔6次〕9.開放討論〔2次〕什么是生物信息學(xué)？Luscombe,N.M.etal.,2001.Whatisbioinformatics?MethodsofInformationinMedicine40:346-358.數(shù)據(jù)挖掘(DataMining)

關(guān)聯(lián)Associating

分類Classifying

建模與模擬Modeling&Simulating

預(yù)測(cè)與檢驗(yàn)Predicting&Testing發(fā)生在Wal*Mart的真實(shí)故事理念：相關(guān)聯(lián)的貨物最好擺在一起問題：啤酒和什么貨物關(guān)聯(lián)？可能的答案：花生米？紅腸？……從上百萬張收銀單獲得的答案：尿布！數(shù)據(jù)倉(cāng)庫(kù)(DataWarehouse)和數(shù)據(jù)挖掘(DataMining)數(shù)據(jù)挖掘流感的預(yù)測(cè)〔網(wǎng)上數(shù)據(jù)挖掘〕具體方法

AutomatedqueryselectionprocessComputationandpre-filteringConstructingtheILI-relatedqueryfractionFittingandvalidatingafinalmodelState-levelmodelvalidationBioinformatics〔CABIOS〕OxfordUniversityPressMPSS://.DomainInformation界面分子生物學(xué)數(shù)據(jù)庫(kù)NCBINationalCenterforBiotechnologyInformation:///全球最大的生物信息資源中心DNA序列、蛋白質(zhì)序列、出版物、數(shù)據(jù)挖掘工具等NCBI主頁(yè)EMBnet北京大學(xué)生物信息學(xué)效勞器BioSino基因組信息資源GenBank(:///)DDBJ(:///)EMBL(/)DDBJEMBL(Germany)EMBL-EBI(UK)蛋白質(zhì)信息資源PDB(:///)PIR(:///)SWISS－PROT(:///)TrEMBL(:///)NRL-3D(:///)密蘇里植物園主頁(yè)P(yáng)DB密蘇里植物園主頁(yè)P(yáng)IR密蘇里植物園主頁(yè)Swiss-Prot&TrEMBL密蘇里植物園主頁(yè)NRL-3DNARNucleicAcidsResearch(分子數(shù)據(jù)庫(kù)專集)NucleicAcidsResearch(效勞器專集)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數(shù)據(jù)庫(kù)組織框架KEGG光合作用代謝通路rbcL基因及一個(gè)光合作用通路蛋白質(zhì)相互作用數(shù)據(jù)庫(kù)〔1〕蛋白質(zhì)相互作用數(shù)據(jù)庫(kù)〔2〕蛋白質(zhì)相互作用數(shù)據(jù)庫(kù)〔3〕蛋白質(zhì)相互作用數(shù)據(jù)庫(kù)〔4〕蛋白質(zhì)相互作用數(shù)據(jù)庫(kù)〔5〕其他數(shù)據(jù)庫(kù)RatGenomeDatabase:///大鼠基因組相關(guān)數(shù)據(jù)專用工具(如VCMap–可視化比較作圖軟件)其他數(shù)據(jù)庫(kù)UTRdb(非翻譯區(qū)數(shù)據(jù)庫(kù)):///有關(guān)3’和5’UTR信息主要的序列數(shù)據(jù)格式FASTAGenBankSwissProtASN.1XMLFASTA格式用于各種FASTA工具簡(jiǎn)要說明之后就是序列沒有注釋信息,只有序列例:>gi|1040960|gb|U35641.1|MMU35641MusmusculusBrca1mRNA,completecdsGGCACGAGGATCCAGCACCTCTCTTGGGGCTTCTCCGTCCTCGGCGCTTGGAAGTACGGATCTTTTTTCTCGGAGAAAAGTTCACTGGAACTGGAAGAAATGGATTTATCTGCCGTCCAAATTCAAGAAGTACAAAATGTCCTTCATGCTATGCAGAAAATCTTAGAGTGTCCGATCTGTTTGGAACTGATCAAAGAACCTGTTTCCACAAAGTGTGACCACATATTTTGCAAATTTTGTATGCTGAAACTTCTTAACCAGAAGAAAGGGCCTTCACAATGTCCTTTGTGTAAGAATGAGATAACCAAAAGGAGCCTACAGGGAAGCACAAGGTTTAGTCAGCTTGCTGAAGAGCTGCTGAGAATAATGGCTGCTTTTGAGCTTGACACGGGAATGCAGCTTACAAATGGTTTTAGTTTTTCAAAAAAGAGAAATAATTCTTGTGAGCGTTTGAATGAGGAGGCGTCGATCATCCAGAGCGTGGGCTACCGGAACCGTGTCAGAAGGCTTCCCCAGGTCGAACCTGGAAATGCCACCTTGAAGGACAGCCTAGGTGTCCAGCTGTCTAACCTTGGAATCGTGAGATCAGTGAAGAAAAACAGGCAGACCCAACCTCGAAAGAAATCTGTCTACATTGAACTAGACTCTGATTCTTCTGAAGAGACAGTAACTAAGCCAGGTGATTGCAGTGTGAGAGACC…

GenBank格式GenBank用純文本文件注釋、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數(shù)據(jù)庫(kù)包括注釋信息例: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類似HTML國(guó)際標(biāo)準(zhǔn)半結(jié)構(gòu)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格式國(guó)際標(biāo)準(zhǔn)半結(jié)構(gòu)化格式用于NCBI數(shù)據(jù)例:Seq-entry::=set{level1,classnuc-prot,descr{title"MusmusculusBrca1mRNA,andtranslatedproducts",source{org{taxname"Musmusculus",db{{db"taxon",tagid10090}},orgname{namebinomial{genus"Mus"