07-1-Genomeanalysis资料.ppt

* Ribosomal RNA (rRNA) is the central component of the ribosome, the protein manufacturing machinery of all living cells * Schematic secondary structure of the two classes of snoRNAs. A) H/ACA box snoRNAs fold into hairpin-hinge-hairpin-tail structures and contain two short sequences called boxes H and ACA, as indicated in the white boxes. The hairpins are interrupted by an internal loop that forms the pseudouridylation pocket. A set of conserved proteins, Nhp2, Gar1, Cbf5 and Nop10, recognize and bind to this structure. B) C/D box snoRNAs show conserved boxes termed C (UGAUGA) and D (CUGA), positioned near their 5 and 3 termini. Sometimes two additional, less conserved, boxes called C and D are present. C and D boxes form a characteristic secondary structure: the K-turn motif. Four evolutionary conserved proteins are associated to it: Snu13 (15.5K in human), that recognizes the internal loop [111], Nop58 and Nop1 (Fibrillarin in human) that cross-link to the U in box C and the U in box D, respectively [112]. In yeast, Nop58 and Snu13 are necessary for the accumulation of all C/D box snoRNAs [113], Nop1 is essential for the production of a subset of box C/D snoRNAs, and Nop56p is not essential for snoRNA accumulation [114]. HMM model for Gene Prediction (Genie) Kulp, D., PhD Thesis, UCSC 2003 (3) 可变剪切的预测 将EST, cDNA序列比对到基因组上 部分有向图算法 3. 比较基因组学 (1) 有功能的通常保守 (2) 例：SUMO底物的预测： a. SUMO化位点存在ψ-K-X-E模体 b. 核定位信号 (NLS) c. 人和小鼠中，SUMO化位点应当保守 d. 功能分析：Gene Ontology (3) 分析结果： a. 2,683个人-小鼠保守的SUMO化底物 b. SUMO化的功能：参与转录调控、信号转导等 Gene Ontology：基因本体论 1. 描述基因/蛋白质的功能 2. 三类术语(Term): a. Cellular component: Where？ b. Biological process: How？ c. Molecular function：What? why？ For example, the gene product cytochrome c can be described by the molecular function term oxidoreductase activity, the biological process terms oxidative phosphorylation and induction of cell death, and the cellular component terms mitochondrial matrix and mitochondrial inner membrane. Gene Ontology：基因本体论 功能显著性分析：超几何分布 转录因