生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources

Bioinformatics (Computational Biology or Information Biology) Computational approaches to answer biological questions 使用電腦來解決生物學的問題 Bioinformatics

Bioformatics covers :  型態、結構、顏色 morphology,color  DNA 及 基因體 genomes  蛋白質、碳水化合物等大分子 Biomacromolecules, proteome  生化、生理、遺傳、演化特性 biochemistry, physiology,genetics,evolution etc.

NTHU 清華大學 生物資訊與網路教學卓越計畫

清華大學 生物資訊與網路教學 卓越計畫

Bioinformatics : Revelations from the Book of Life …….BIOHRIACGTDSTRONGJKWISEGT TUSH……MLGHSINCERITYGKJ……….. CANCER ……...FEBEAUTYRANTGGGGCUP………

Bioinformatics Information can be converted into knowledge Promote human civilization and science achievements Creat knowledge-based economics

Bioinformatics (Computational Biology or Information Biology) Why does it emerge so rapidly ? 1. Explosion of sequence and structural information 2. Advancement of Internet Bioinformatics

The Three Projects Affecting Human Civilization most Menhatten Project 1940s Apollo Project 1965s Human Genome Project

Human Genome Project Unravelling the 3 x 10 9 bp genome Goals 1. Understanding Life Science 2. Disease Diagnosis and Treatment Legal and Ethical Challenges 1. Human rights 2. Health insurance

GOLD (Genomes OnLine Database)

Internet (International Network) ARPAnet (created by Defense Advanced Research Projects Agency), cold war network Usenet ( the first News Distribution protocol) TCP/IP (Transmission Control Protocol/ Internet Protocol), with routing capability NSFnet (TCP/IP based, connecting university supercomputers, evolved into Inernet today) Commercial links to Internet, and popularization of WWW

Major Tasks of Bioinformatics 1. Establish data base 2. Search/retrieve bioinformations 3. Analysis of bioinformations

From independent works to unified actions 1. Database 2. Data Retrieval 3. Data Analysis

Major Disciplines Algorithm, Graphics, Signal Processing, Statistics, Simulation, Computer Architecture, Database Management, Artificial Intelligence… Biochemistry, Molecular Biology, Genomics, Proteomics, Physical Chemistry, Structural Biology/Physics

Applications Database Construct, Database Query, Genome Mapping and Comparison, Gene Identification and Annotation Sequence Alignment, Molecular Evolution Structure Alignment and Comparison, Structure Prediction, Structure-Based Drug Design, Molecular Modeling and Simulation

Gene Annotation Gene Annotation 定序 DNA Sequencing 組合 Assemble DNA Sequence 確認基因 Gene Identification 功能註解 Gene Annotation 資料庫 GenBank 使用分析 Retrieval and Analysis

NCBI (National Center for Biotechnology Information) Established (1988) by US Congress 1. System for storing and analyzing 2. Advancing methods for data retrieval and analysis 3. Facilitation of the use

NCBI NCBI 1. Database : GenBank 2. Database Retrieval Entrez, PubMed, Locus Link, Taxonomy Browser 3. Data Analysis BLAST, Electronic PCR, ORF Finder, UniGene, dbSNP, Human Genome Sequencing, Human MapViewer, Intrer Genomes, Cancer Chromosome Aberration Project (CCAP), Gene Expression Omnibus (GEO), Online Online Mendelian Inheritance in Man (OMIM), The Molecular Modeling DataBase (MMDB), and the Conserved Domain Database (CDD).

GenBank Created (1982) by NIGMS/NIH Los Alamos National Lab - annotates & organizes IntelliGenetics (1987-) NCBI (1988-)

NCBI

Human Genome, Alzheimer disease

Human Genome Map, Presenilin 2 ( Alzheimer disease 4)

NCBI - ORF Finder, M. hyopneumoniae PTSI

NCBI – ORF Finder, PTSI

NCBI – BLAST, PTSI

NCBI – Structure, MMDB, PTSI

NCBI – Cn3D, PTSI structure

ExPASy

ExPASy - 2 ExPASy - 2 o structure prediction, GOR IV, PTSI

ExPASy – 2 ExPASy – 2 o structure prediction, GOR IV, PTSI

ExPASy – Topology prediction, SOSUI

PDB

PDB

Web Resources Organization : NCBI/NIH, EBI/EMBL, SIB Database : GenBank, ExPASy, PDB Societies/Agencies : WHO, ASM Universities : NIH, CDC, Pasteur, 國衛院, 高 速電腦中心, 清華, 陽明 Firms : Celera, Human Genome Sciences

Conclusion Tremendous information on the web Promote biological sciences Solving problems and creating new hints/problems Use the information and generate new information