Department of Life Science

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Bioinformatics and Web Resources
David Shiuan

• Department of Life Science
• Institute of Biotechnology
• National Dong Hwa University

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Bioinformatics(Computational Biology or
Information Biology)
Bioinformatics

• Computational approaches to
• answer biological questions
• ?????????????

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Bioformatics covers

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

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NTHU???? ?????????????
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Bioinformatics Revelations from the Book of
Life

• .BIOHRIACGTDSTRONGJKWISEGT
• TUSHMLGHSINCERITYGKJ..
• CANCER
• ...FEBEAUTYRANTGGGGCUP

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Bioinformatics

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

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Bioinformatics(Computational Biology or
Information Biology)
Bioinformatics

• Why does it emerge so rapidly ?
• 1. Explosion of sequence and
• structural information
• 2. Advancement of Internet

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The Three Projects Affecting Human Civilization
most

• Menhatten Project 1940s
• Apollo Project 1965s
• Human Genome Project
• 1993-2003

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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

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GOLD (Genomes OnLine Database)
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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

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Major Tasks of Bioinformatics

• 1. Establish data base
• 2. Search/retrieve bioinformations
• 3. Analysis of bioinformations

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From independent works to unified actions

1. Database
2. Data Retrieval
3. Data Analysis

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Major Disciplines

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

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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

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Gene Annotation

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

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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

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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).

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GenBank

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

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NCBI
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Human Genome, Alzheimer disease
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Human Genome Map, Presenilin 2 ( Alzheimer
disease 4)
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NCBI - ORF Finder, M. hyopneumoniae PTSI
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NCBI ORF Finder, PTSI
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NCBI BLAST, PTSI
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NCBI Structure, MMDB, PTSI
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NCBI Cn3D, PTSI structure
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ExPASy
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ExPASy - 2o structure prediction, GOR IV, PTSI
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ExPASy 2o structure prediction, GOR IV, PTSI
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ExPASy Topology prediction, SOSUI
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ExPASy Topology prediction, SOSUI
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ExPASy Topology prediction, SOSUI
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PDB
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PDB
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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

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Conclusion

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