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Department of Life Science

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Bioinformatics and Web Resources David Shiuan Department of Life Science Institute of Biotechnology – PowerPoint PPT presentation

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Title: Department of Life Science


1
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?????????
Bioinformatics and Web Resources
David Shiuan
  • Department of Life Science
  • Institute of Biotechnology
  • National Dong Hwa University

2
Bioinformatics(Computational Biology or
Information Biology)
Bioinformatics
  • Computational approaches to
  • answer biological questions
  • ?????????????

3
Bioformatics covers
  1. ???????? morphology,color
  2. DNA ? ??? genomes
  3. ????????????? Biomacromolecules, proteome
  4. ????????????? biochemistry, physiology,genetics,ev
    olution etc.

4
NTHU???? ?????????????
5
???? ????????? ????
6
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7
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8
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9
Bioinformatics Revelations from the Book of
Life
  • .BIOHRIACGTDSTRONGJKWISEGT
  • TUSHMLGHSINCERITYGKJ..
  • CANCER
  • ...FEBEAUTYRANTGGGGCUP

10
Bioinformatics
  • Information can be converted into
  • knowledge
  • Promote human civilization and
  • science achievements
  • Creat knowledge-based economics

11
Bioinformatics(Computational Biology or
Information Biology)
Bioinformatics
  • Why does it emerge so rapidly ?
  • 1. Explosion of sequence and
  • structural information
  • 2. Advancement of Internet

12
The Three Projects Affecting Human Civilization
most
  • Menhatten Project 1940s
  • Apollo Project 1965s
  • Human Genome Project
  • 1993-2003

13
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

14
GOLD (Genomes OnLine Database)
15
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16
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17
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

18
Major Tasks of Bioinformatics
  • 1. Establish data base
  • 2. Search/retrieve bioinformations
  • 3. Analysis of bioinformations

19
From independent works to unified actions
  1. Database
  2. Data Retrieval
  3. Data Analysis

20
Major Disciplines
  • Algorithm, Graphics, Signal Processing,
    Statistics, Simulation, Computer Architecture,
    Database Management, Artificial Intelligence
  • Biochemistry, Molecular Biology, Genomics,
    Proteomics, Physical Chemistry, Structural
    Biology/Physics

21
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

22
Gene Annotation
  • ?? DNA Sequencing
  • ?? Assemble DNA Sequence
  • ???? Gene Identification
  • ???? Gene Annotation
  • ??? GenBank
  • ???? Retrieval and Analysis

23
NCBI (National Center for Biotechnology
Information)
  • Established (1988) by US Congress
  • System for storing and analyzing
  • Advancing methods for data retrieval and analysis
  • Facilitation of the use

24
NCBI
  • Database GenBank
  • Database Retrieval
  • Entrez, PubMed, Locus Link, Taxonomy Browser
  • 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).

25
GenBank
  • Created (1982) by NIGMS/NIH
  • Los Alamos National Lab
  • - annotates organizes
  • IntelliGenetics (1987-)
  • NCBI (1988-)

26
NCBI
27
Human Genome, Alzheimer disease
28
Human Genome Map, Presenilin 2 ( Alzheimer
disease 4)
29
NCBI - ORF Finder, M. hyopneumoniae PTSI
30
NCBI ORF Finder, PTSI
31
NCBI BLAST, PTSI
32
NCBI Structure, MMDB, PTSI
33
NCBI Cn3D, PTSI structure
34
ExPASy
35
ExPASy - 2o structure prediction, GOR IV, PTSI
36
ExPASy 2o structure prediction, GOR IV, PTSI
37
ExPASy Topology prediction, SOSUI
38
ExPASy Topology prediction, SOSUI
39
ExPASy Topology prediction, SOSUI
40
PDB
41
PDB
42
Web Resources
  • Organization NCBI/NIH, EBI/EMBL, SIB
  • Database GenBank, ExPASy, PDB
  • Societies/Agencies WHO, ASM
  • Universities NIH, CDC, Pasteur, ???, ??????,
    ??, ??
  • Firms Celera, Human Genome Sciences

43
Conclusion
  • Tremendous information on the web
  • Promote biological sciences
  • Solving problems and creating new
  • hints/problems
  • Use the information and generate
  • new information
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