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1、第六章基因预测和基因结构分析 I 生物信息学 http www bio davidson edu courses genomics method shotgun html 基因组测序策略 Genomesequencing QUICKER SMALLER CHEAPER NatureBiotechnology26 1135 1145 2008 13years 3billion http www ncbi nlm nih gov genomes static gpstat html NatureBiotechnology26 1135 1145 2008 identifyingnewgenes l
2、ookingatchromosomeorganizationandstructure findinggeneregulatorysequences comparativegenomics Applicationsofsequencing WherearetheGenesintheGenome GAGAAAATCAATTGGTTTAGAAGGTTTGGACTCACTTGACAGGTTCAGTTGGAGACGATCATAGGTGGCTGCTGTGACAAAGGGAAATTGTGCTTTTCCAGCATGCTTACTGACCCTGATTTACCTCAGGAGTTTGAAAGGATGTCTTCCAAG
3、CGACCAGCCTCTCCGTATGGGGAAGCAGATGGAGAGGTAGCCATGGTGACAAGCAGACAGAAAGTGGAAGAAGAGGAGAGTGACGGGCTCCCAGCCTTTCACCTTCCCTTGCATGTGAGTTTTCCCAACAAGCCTCACTCTGAGGAATTTCAGCCAGTTTCTCTGCTGACGCAAGAGACTTGTGGCCATAGGACTCCCACTTCTCAGCACAATACAATGGAAGTTGATGGCAATAAAGTTATGTCTTCATTTGCCCCACACAACTCATCTACCTCACCTCAGAAGGCAGAAGAAGGTGGG
4、CGACAGAGTGGCGAGTCCTTGTCTAGTACAGCCCTGGGAACTCCTGAACGGCGCAAGGGCAGTTTAGCTGATGTTGTTGACACCTTGAAGCAGAGGAAAATGGAAGAGCTCATCAAAAACGAGCCGGAAGAAACCCCCAGTATTGAAAAACTACTCTCAAAGGACTGGAAAGACAAGCTTCTTGCAATGGGATCGGGGAACTTTGGCGAAATAAAAGGGACTCCCGAGAGCTTAGCTGAGAAAGAAAGGCAACTCATGGGTATGATCAACCAGCTGACCAGCCTCCGAGAGCAGCTGTTG
5、GCTGCCCACGATGAGCAGAAGAAACTAGCTGCCTCTCAGATTGAGAAACAGCGTCAGCAAATGGAGCTGGCCAAGCAGCAACAAGAACAAATTGCAAGACAGCAGCAGCAGCTTCTACAGCAACAACACAAAATCAATTTGCTCCAGCAACAGATCCAGGTTCAAGGTCAGCTGCCGCCATTAATGATTCCCGTATTCCCTCCTGATCAACGGACACTGGCTGCAGCTGCCCAGCAAGGATTCCTCCTCCCTCCAGGCTTCAGCTATAAGGCTGGATGTAGTGACCCTTACCCTGTTCAG
6、CTGATCCCAACTACCATGGCAGCTGCTGCCGCAGCAACACCAGGCTTAGGCCCACTCCAACTGCAGCAGTTATATGCTGCCCAGCTAGCTGCAATGCAGGTATCTCCAGGAGGGAAGCTGCCAGGCATACCCCAAGGCAACCTTGGTGCTGCTGTATCTCCTACCAGCATTCACACAGACAAGAGCACAAACAGCCCACCACCCAAAAGCAAGGATGAAGTGGCACAGCCACTGAACCTATCAGCTAAACCCAAGACCTCTGATGGCAAATCACCCACATCACCCACCTCTCCCCATATG
7、CCAGCTCTGAGAATAAACAGTGGGGCAGGCCCCCTCAAAGCCTCTGTCCCAGCAGCGTTAGCTAGTCCTTCAGCCAGAGTTAGCACAATAGGTTACTTAAATGACCATGATGCTGTCACCAAGGCAATCCAAGAAGCTCGGCAAATGAAGGAGCAACTCCGACGGGAACAACAGGTGCTTGATGGGAAGGTGGCTGTTGTGAATAGTCTGGGTCTCAATAACTGCCGAACAGAAAAGGAAAAAACAACACTGGAGAGTCTGACTCAGCAACTGGCAGTTAAACAGAATGAAGAAGGAAAA
8、TTTAGCCATGCAATGATGGATTTCAATCTGAGTGGAGATTCTGATGGAAGTGCTGGAGTCTCAGAGTCAAGAATTTATAGGGAATCCCGAGGGCGTGGTAGCAATGAACCCCACATAAAGCGTCCAATGAATGCCTTCATGGTGTGGGCTAAAGATGAACGGAGAAAGATCCTTCAAGCCTTTCCTGACATGCACAACTCCAACATCAGCAAGATATTGGGATCTCGCTGGAAAGCTATGACAAACCTAGAGAAACAGCCATATTATGAGGAGCAAGCCCGTCTCAGCAAGCAGCACCTG
9、GAGAAGTACCCTGACTATAAGTACAAGCCCAGGCCAAAGCGCACCTGCCTGGTGGATGGCAAAAAGCTGCGCATTGGTGAATACAAGGCAATCATGCGCAACAGGCGGCAGGAAATGCGGCAGTACTTCAATGTTGGGCAACAAGCACAGATCCCCATTGCCACTGCTGGTGTTGTGTACCCTGGAGCCATCGCCATGGCTGGGATGCCCTCCCCTCACCTGCCCTCGGAGCACTCAAGCGTGTCTAGCAGCCCAGAGCCTGGGATGCCTGTTATCCAGAGCACTTACGGTGTGAAAGGA
10、GAGGAGCCACATATCAAAGAAGAGATACAGGCCGAGGACATCAATGGAGAAATTTATGATGAGTACGACGAGGAAGAGGATGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATATTGCAG Genes i e proteincoding But only 2 ofthehumangenomeencodesproteinsOtherthanproteincodinggenes whatisthere genesfornoncodingRNAs rRNA tRNA miRNAs etc structuralsequences sca
11、ffoldattachmentregions regulatorysequencesnon functional junk It sstilluncertain controversialhowmuchofthegenomeiscomposedofanyoftheseclassesTheanswerswillcomefromexperimentationandbioinformatics Complexityofgenome PublishedbyAAAS Science306 636 640 2004 TheENCODEProject ENCyclopediaOfDNAElements ht
12、tp genome ucsc edu ENCODE Proteincodinggenes InlongopenreadingframesORFsinterruptedbyintronsineukaryotesTakeupmostofthegenomeinprokaryotes butonlyasmallportionoftheeukaryoticgenomeRNA onlygenesTransferRNA ribosomalRNA snoRNAs guideribosomalandtransferRNAmaturation intronsplicing guidingmRNAstothemem
13、branefortranslation generegulation thisisagrowinglistGenecontrolsequencesPromotersRegulatoryelementsTransposableelements bothactiveanddefectiveDNAtransposonsandretrotransposonsManytypesandsizesRepeatedsequences CentromeresandtelomeresManywithunknown orno functionUniquesequencesthathavenoobviousfunct
14、ionAsageneralrule eachpartofagenomicsequencehasonlyonefunction protein codinggene RNAgene controlsignal transposableelement repeatsequence maybenofunctionalatall But mostsequenceelementsoverlaponlyslightlyifatall What sinagenome protein codinggenes non protein codinggenes easiertofindthanotherfuncti
15、onalelementswhy genesaretranscribed whichmeansthatwecanidentifythembylookingatRNAtraditionallythishasbeendonebycDNAorESTsequencing morerecentlybymicroarray SAGE MPSS etc protein codinggeneshaverecognizablefeaturesopenreadingframes ORFs codonbiasknowntranscriptionandtranslationalstartandstopmotifs pr
16、omoters 3 poly Asites spliceconsensussequencesatintron exonboundaries Findingprotein codinggenes Findingnon protein codinggenes e g tRNA rRNA snoRNA miRNA variousotherncRNAsHardertofindthanprotein codinggenesWhy oftennotpoly Atailed don tendupincDNAlibrariesnoORFconstraintonsequencedivergenceatnucleotidenotproteinlevel sohomologyishardertodetectSo howdowefindthese secondarystructurehomology especiallyalignmentofrelatedspeciesexperimentallyisolationthroughnon polyAdependentcloningmethodsmicroarra
