Download Bioinformatics & Web Resource

生物資訊與網路資源
Bioinformatics and Web Resources
David Shiuan
Department of Life Science
Institute of Biotechnology
National Dong Hwa University
Bioinformatics
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
Bioformatics 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.
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
Bioinformatics
(Computational Biology
or Information Biology)
Why does it emerge so rapidly ?
1. Explosion of sequence and
structural information
2. Advancement of Internet
The Three Projects Affecting
Human Civilization most
Menhatten Project 1940s
Apollo Project 1965s
Human Genome Project
1993-2003
Human Genome Project
1990-2003
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 (Genomes OnLine Database)
Internet (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 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
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
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 - 2o structure prediction, GOR IV, PTSI
ExPASy – 2o structure prediction, GOR IV, PTSI
ExPASy – Topology prediction, SOSUI
ExPASy – Topology prediction, SOSUI
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