生物信息学在科学研究中的运用分析.ppt

生物信息学在医学科学研究中的运用 生物信息学 生物信息学是一门生命科学与计算机科学相互渗透形成的新兴交叉学科。 利用计算机和网络去获取、组织、处理、储存、分析和解释生物学数据内在的信息，并阐明它们包含的生物学意义，提取生物学新知识、新规律。 生物信息学的研究领域: ①生物学数据库的建立和管理以及数据库接口 和检索工具的研制 ②序列对比，它是生物信息学的基础 ③蛋白质的2级、3级结构预测和功能预测 ④计算机辅助基因识别 ⑤DNA语言包括非编码区序列的分析 ⑥分子进化和比较基因组学 ⑦序列重叠群的拼接 ⑧ DNA芯片和微阵列的发展 Molecular Databases Primary Databases Original submissions by experimentalists Database staff organize but don’t add additional information Example: GenBank Derivative Databases Human curated compilation and correction of data Example: SWISS-PROT, NCBI RefSeq mRNA Computationally Derived Example: UniGene Combinations Example: NCBI Genome Assembly Primary biological databases Nucleic acid EMBL GenBank DDBJ (DNA Data Bank of Japan) Protein PIR MIPS SWISS-PROT TrEMBL NRL-3D What is GenBank? NCBI’s Primary Sequence Database Nucleotide only sequence database GenBank Data Direct submissions individual records (BankIt, Sequin) Batch submissions via email (EST, GSS, STS) ftp accounts sequencing centers Data shared three collaborating databases GenBank DNA Database of Japan (DDBJ). European Molecular Biology Laboratory Database (EMBL) at EBI. EMBL/GenBank/DDJB These 3 db contain mainly the same information (few differences in the format and syntax) Serve as archives containing all sequences (single genes, ESTs, complete genomes, etc.) derived from: Genome projects and sequencing centers Individual scientists Patent offices (i.e. USPTO, EPO) Non-confidential data are exchanged daily Currently: 2.5 x107 sequences, over 3.2 x1010 bp; Sequences from 50,000 different species; Databases related to Genomics Contain information on genes, gene location (mapping), gene nomenclature and links to sequence databases; Exist for most organisms important for life science research; Examples: MIM, GDB (human), MGD (mouse), FlyBase (Drosophila), SGD (yeast), MaizeDB (maize), SubtiList (B.subtilis), etc. Format: generally relational (Oracle, SyBase or AceDb). Swiss-Prot Annotate