复旦大学：计算机预测真核生物基因组中的基因 Predicting Genes in Eukaryotic Genomes By Computer（郝柏林）

Predicting Genes in Eukaryotic Genomes By computer Hao bailin(郝柏林) T-Life research Center, Fudan University Beijing Genomics Institute, Academia sinica Institute of Theoretical Physics, Academia Sinica (www.itp.ac.cn/hao/

Predicting Genes in Eukaryotic Genomes By Computer Hao Bailin (郝柏林) T-Life Research Center, Fudan University Beijing Genomics Institute , Academia Sinica Institute of Theoretical Physics, Academia Sinica (www.itp.ac.cn/~hao/)

The Central Dogma of molecular Biology replication DNA DNA reverse transcription transcription CDNA mrNA translation Protein/Enzyme folding Function Structure Interaction

The Central Dogma of Molecular Biology replication DNA DNA reverse transcription transcription cDNA mRNA translation Protein/Enzyme folding Function Structure interaction

Eukaryote Prokaryote 10∞m Nucleolus Nucleoid capsule Cell wall Nucleus Ribosomes Cell membrane Flagellum Mitochondrion

Human family Nuclear genome 力 Mitochondrial genomes o

2 4 5 6 8 9 101112 自 131415161718 192021 22

DNA(脱氧核糖核酸)序列 由4种字母(核苷酸、碱基a,c,g,t)组成 长度:单条染色体从几千到几千万个字母 ·人有23对染色体;黑猩猩有24对;小鼠有 19对;水稻有12对;猕猴桃有300对 ·染色体的一部分编码蛋白质;其余是控制 信号,重复片段,意义不明的“随机”字 母串,等等

DNA(脱氧核糖核酸)序列 • 由4种字母(核苷酸、碱基a, c, g, t )组成 • 长度：单条染色体从几千到几千万个字母 • 人有23对染色体；黑猩猩有24对；小鼠有 19对；水稻有12对；猕猴桃有300对 • 染色体的一部分编码蛋白质；其余是控制 信号，重复片段，意义不明的“随机”字 母串，等等

Large-Scale DNA Sequencing Since 1977 Sanger method polymerization stopping Maxam-Gilbert: chemical degradation Each reaction: 500-600 bp(a single read) Clone by clone vs. whole-genome shotgun Sequence assembling: reads -contigs scattolds-superscaffolas Automatic sequencer: MegaBace, 96 or 384 channels

Large-Scale DNA Sequencing Since 1977 • Sanger method: polymerization stopping • Maxam-Gilbert: chemical degradation • Each reaction: 500-600 bp (a single read) • Clone by clone vs. whole-genome shotgun • Sequence assembling: reads – contigs – scaffolds – superscaffolds • Automatic sequencer: MegaBace, 96 or 384 channels

Letter production at BGi (Beijing Hangzhou) Daily: 5X10 Yearly: 100

Letter production at BGI (Beijing + Hangzhou) Daily: 5 x107 Yearly: 1010

已经测序的真核生物基因组 酿酒酵母( Saccharomyces cerevisiae) 列解酵母( Schizosaccharomyces pombe) 秀丽线虫( Caenorhabitatis elegans) 果蝇( Drosophila melanogaster 恶性疟疾原虫( Plasmodium falciparum) 岗比亚按蚊( Anopheles gambiae) 智人( Homo sapiens)、黑猩猩( Pan troglodytes 小鼠( Mus musculus)、大鼠( Rattus norvegicus) 家犬( Canis familiaris)、家鸡( Gallus gallus))、家猪( Sus scrofa) 河豚鱼( Fugu rubripes)) 家蚕( Bambyx mori)、蜜蜂( Apsis mellifera) 拟南芥( Arabidopsis thaliana)、水稻( Oryza sativa) 玉米( ea mays

已经测序的真核生物基因组 • 酿酒酵母 (Saccharomyces cerevisiae) • 列解酵母 (Schizosacchromyces pombe) • 秀丽线虫 (Caenorhabitatis elegans) • 果蝇 (Drosophila melanogaster) • 恶性疟疾原虫 (Plasmodium falciparum) • 岗比亚按蚊 (Anopheles gambiae) • 智人 (Homo sapiens)、黑猩猩 (Pan trogodytes) • 小鼠 (Mus musculus)、大鼠 (Rattus norvegicus) • 家犬 (Canis familiaris)、家鸡 (Gallus gallus)、家猪(Sus scrofa) • 河豚鱼 (Fugu rubripes) • 家蚕 (Bambyx mori)、蜜蜂 (Apsis mellifera) • 拟南芥(Arabidopsis thaliana)、水稻(Oryza sativa) • 玉米 (Zea mays)

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agaaaaaatctgggacggaaggattcgaacctccgagtaacgggaccaaaacccgctgccttaccacttggccacgccccatttcgggttttatgcgacactaataaacagtattatgtttattt cttattcgtcaatcctacttcaattacataaaaatggggggtattctcttggtaggattctagacat gcgaataatatagaatccaaaaaatgcattgatcattacatggaattctattaagatattatatgaaagtcgaatttcttccactctcatttgagagtgcgaatacaaggaggtattttgtgttt gggaaagtccgaagaaaaaaggattttgaatcctccttttcctttttcccttagaaaaataactcaatcaa aatccaattatctactctacaagaacgaaacgcttgttatgcctaatatacttagtttaacctgtatttgttttaattctgttatttatccgactagttttttcttcgccaaattgcccgaagct tatgccattttcaatccaatcgtggattttatgcctgtcatacctgtactcttttttctattagcctttgtttggcaag ctgctgtaagttttcgatgaaatctttactactctgtctgccaaattgaatcatgtattcattctaaaaaaattcgaaaaatggataagagccgagaagtcttatattatgaaccttcgattctaaaattcaaattcttctacattgaatgtatagctgcagcaataaatttggatcagcctttctactccctgcatc tacgttgagcaggtatctttaggtaaccgcacaatacctaacctaatttattgataagagt gcttattataaatcaattcttgcaatttttttcaaaaattgatttttgcatttttaggtgtcaaaataaacaaaacccatcctagtggatttgtgtggtaaggaaaaacgggtaatctattccttaaaaaaaaatct tggagattatgtaatgcttactctcaaactttttgtttatacagtagtgatattctttgtttccctctttatctttggattcttatctaatgatccaggacgtaatcctgggcgt gacgagtaaaaatccaaaattttttcttacaaattggatttgtttcatacatttatctacgagaaaatccgggggtcagaattcctt ccaattcgaaagtcccaaacgatccgagggggcggaaagagagggattcgaaccctcggtacaaaaaaattgtacaacggattagcaatccgccgctttagtccactcagccatctctccccgtt ccaaatcgaaaggtttccgtgatatgacagaggcaagaaataacgattgcaaaaaatcc ttcctttttctttcaaaagttcaaaaaaattatattgccaattccattttagttatattcttttttcttaatgttaataaaaaaaagaagaaaattcttcttttttctttctaattctaaaattggatattggctaaaagacaatcagatagattttctcttcagcaggcatttccatataggacttgttataataaaacaagca ggttatagaaaaaaactcttttttttattatttatcaacaaagcaaaaaggggtcttatcaaaccaacccaccccataaaattggaaagaaagataaagtaagtggacctgactccttgaat gaggcctctatccgctattctgatatataaattcgatgtagatgaaattgtataagtggatttttttgtatttc cttagacttagaccacgcaaggcaagaatttctcgctatttactatttcatattcttgttactagatgttctataggaataagaagaaatcgcaacccctttccgctacacataaaaatggattt cgaaagtcaatttttcttttcaatatctttactttttttcagaatcctatttttgttcttatacccatgcaataga gagcgagtgggaaaagggaggttactttttttcattttttccttaaaaaataggctttcttggaaataggaatcatggaataatctgaattccaatgtttatttctatagtataagaaaaactaattgaatcaaattcatggatttaccacgacctcggct gtgaccccatagataaaaatgcaaaatttctatct tcgagaccattgaaaaaaggcattgaacgagaaaaaatcgtccacagataatctatcgtatgccttggaagtgatataaggtgctcggaaat ggttgaagtaattgaataggaggatcactatga ctatagcccttggtagagttactaaagaagaaaat gatttatttgatattatggacgactggtta cgaagggaccgttttgtttttgtaggatggtctggcctattgctttttccttgtgcttatttcgctttaggaggttggtttacagggacaacttttgtaacttcttggtatacccatggattggc gagttcctatttggaaggttgcaatttcttaaccgcagcagtttccacccct gccaatagtttagcacactct ttgttgctactatggggcccggaagcacaaggggattttactcgttggtgtcaattaggt ggtctgtggacttttgttgctctccatggggcttttgcactaataggtttcatgttacgtcaatt tgaacttgctcggtctgttcaattgcggccttataatgcaatttcattctctggcccaatcgctgtttttgttt ccgtattcctgatttatccactggggcaatccggttggttctttgcgccgagttttggcgtagcagcgatatttcgattcatcctcttcttccaaggatttcataattggacgttgaacccattt catatgatgggagttgccggagtattaggcgcggctctgctatgcgctattcatggggcaaccgtgga