基因组分析.pptVIP

* * * Piwi蛋白家族，为无脊椎动物的精子和干细胞的发育所必需 * 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]. (2) 基因预测 基本原理： 序列同源比对：与数据库中已知的序列（如EST， cDNA，蛋白质序列）一致或相似?预测新基因 从头预测(ab initio)：依据基因的特征序列，如原核生物的长ORF、真核生物编码区中外显子和内含子间的GT-AG规则、基因5’端的CpG岛、核心启动子的TATA盒、起始密码子两侧的特征序列、3’端的polyA尾等?统计分析，识别基因 以上两种方法的结合 真核生物的基因结构 5’ 3’ 3’ 5’ ~ 1-100 Mbp 5’ 3’ 3’ 5’ … … … … ~ 1-1000 kbp exons (cds utr) / introns (~ 102-103 bp) (~ 102-105 bp) Polyadenylation site promoter (~103 bp) enhancers (~101-102 bp) other regulatory sequences (~ 101-102 bp) 其他相关术语 CDS (Coding sequence): The portion of DNA that codes for transcription of messenger RNA. ORF (Open Reading Frame): 从AUG开始，至stop codon终止 Codon Usage: CAI … 基因预测常见方法 序列相似性比较方法 模式生物基因组全测序完成及大规模EST测序，为相似性比较预测法提供了基础。 近一半脊椎动物基因可通过与模式生物序列比较，找到高相似性序列。 不足：很多情况下，不能识