生物資訊與網路資源生物資訊與網路資源

Department of Life Science Institute of BiotechnologyNational Dong Hwa University

David Shiuan

生物資訊與網路資源生物資訊與網路資源Bioinformatics and Web ResourcesBioinformatics and Web Resources

BioinformaticsBioinformatics(Computational Biology (Computational Biology

or Information Biology)or Information Biology)

Computational approaches to

answer biological questions

使用電腦來解決生物學的問題

BioinformaticsBioinformatics

BioformaticsBioformatics covers :covers :

1. 型態、結構、顏色 morphology,color

2. DNA 及 基因體 genomes

3. 蛋白質、碳水化合物等大分子 Biomacromolecules, proteome

4. 生化、生理、遺傳、演化特性 biochemistry, physiology,genetics,evolution etc.

NTHUNTHU 清華大學 生物資訊與網路教學卓越計清華大學 生物資訊與網路教學卓越計畫畫

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 : Bioinformatics : Revelations from Revelations from the Book of Lifethe Book of Life

…….BIOHRIACGTDSTRONGJKWISEGT

TUSH……MLGHSINCERITYGKJ……….. CANCER

……...FEBEAUTYRANTGGGGCUP………

BioinformaticsBioinformatics

Information can be converted into

knowledge

Promote human civilization and

science achievements

Creat knowledge-based economics

BioinformaticsBioinformatics(Computational Biology (Computational Biology

or Information Biology)or Information Biology)

Why does it emerge so rapidly ?

1. Explosion of sequence and structural information

2. Advancement of Internet

BioinformaticsBioinformatics

The Three Projects Affecting The Three Projects Affecting Human Civilization mostHuman Civilization most

Menhatten Project 1940s

Apollo Project 1965s

Human Genome Project 1993-2003

Human Genome ProjectHuman Genome Project 1990-20031990-2003

Unravelling the 3 x 109 bp genome

Goals 1. Understanding Life Science 2. Disease Diagnosis and Treatment Legal and Ethical Challenges 1. Human rights 2. Health insurance

GOLD GOLD (Genomes OnLine Database)(Genomes OnLine Database)

Internet Internet (International Network)(International Network)

1972 - ARPAnet (created by Defense Advanced Research Projects Agency), cold war network

1979 - Usenet (the first News Distribution protocol)

1982 - TCP/IP (Transmission Control Protocol/ Internet Protocol), with routing capability

1987 - NSFnet (TCP/IP based, connecting university supercomputers, evolved into Inernet today)

1990 - Commercial links to Internet, and popularization of WWW

Major Tasks of Major Tasks of BioinformaticsBioinformatics

1. Establish data base

2. Search/retrieve bioinformations

3. Analysis of bioinformations

From independent works From independent works to unified actionsto unified actions

1. Database

2. Data Retrieval

3. Data Analysis

Major DisciplinesMajor Disciplines

Algorithm, Graphics, Signal Processing, Statistics, Simulation, Computer Architecture, Database Management, Artificial Intelligence…

Biochemistry, Molecular Biology, Genomics, Proteomics, Physical Chemistry, Structural Biology/Physics

ApplicationApplicationss

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 AnnotationGene 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

NCBINCBI (National Center for (National Center for Biotechnology Information)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

NCBINCBI1. Database : GenBank

2. Database Retrieval Entrez, PubMed, Locus Link, Taxonomy Browser

3. Data Analysis BLAST, Electronic PCR, ORF Finder, UniGene, dbS

NP, 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).

GenBankGenBank

Created (1982) by NIGMS/NIH

Los Alamos National Lab - annotates & organizes

IntelliGenetics (1987-)

NCBI (1988-)

NCBINCBI

Human Genome, Human Genome, Alzheimer diseaseAlzheimer disease

Human Genome Map, Human Genome Map, Presenilin 2 ( Alzheimer disease 4)Presenilin 2 ( Alzheimer disease 4)

NCBI - ORF Finder, NCBI - ORF Finder, M. hyopneumoniaeM. hyopneumoniae PTSI PTSI

NCBI – ORF Finder, PTSINCBI – ORF Finder, PTSI

NCBI – BLAST, PTSINCBI – BLAST, PTSI

NCBI – Structure, MMDB, PTSINCBI – Structure, MMDB, PTSI

NCBI – Cn3D, PTSI structureNCBI – Cn3D, PTSI structure

ExPASyExPASy

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

ExPASy –ExPASy – 22o structure prediction, GOR IV, PTSI

ExPASy – Topology prediction, SOSUI

ExPASy – Topology prediction, SOSUI

ExPASy – Topology prediction, SOSUI

PDBPDB

PDBPDB

Web ResourcesWeb 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

ConclusionConclusion

Tremendous information on the web

Promote biological sciences

Solving problems and creating new hints/problems

Use the information and generate new information