Course Introduction

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					Bioinformatics

      Course Introduction
About Bioinformatics
 Bioinformatics (                         )
•   How to learn?
•   Three major parts you should know about
    bioinformatics:
    ๏   General theories and applications.
        How to use online tools and free-ware software to analyze
        data?
        What are theories behind these tools?
    ๏   Developmental tools.
        To develop algorithms and software for data mining.
        To establish databases.
    ๏   Genomics, Proteomics and Systems Biology.
        What are critical questions?
        What is the knowledge derived from bioinformatics?
        What are future directions?
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About this course

  The name
 •   Bioinformatics (          )

  The place
 •   LS 114 (Theory)
 •           ST021(Practice)




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About this course

  Two parts in this course:
 •   The theoretical part, and
 •   The practical part.

  The aims of this course
 •   To understand what bioinformatics is.
 •   To go through major topics of bioinformatics.
 •   To learn basic skills of bioinformatics.




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The requirements of this course

  You should have basic knowledge and
  understanding of general biology.

  You should have basic knowledge and
  understanding of molecular biology.

  You should have basic knowledge of
  computer and internet surfing.



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The materials of this course

  The textbooks.

 •   Bioinformatics:A Practical Guide to the Analysis of
     Genes and Proteins 3/e 2005

 •   Understanding Bioinformatics 2008 (Recommended)

  The home page of this course.

 •   http://140.128.117.125


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What topics we will go through?

  There are four major topics we will go
  through:

 (1) Introduction to bioinformatics and computer skills
     you have to know.
 (2) Understanding and usage of biological databases.
 (3) Sequence analysis of DNA and protein.
 (4) Comparative genomics.




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Topic 1.

  Introduction to bioinformatics and
  computer skills you have to know:
 •   A general introduction to bioinformatics.
     ๏   The big picture of bioinformatics.
     ๏   What is in bioinformatics?
     ๏   What are they doing in bioinformatics?
     ๏   The applications of bioinformatics.
 •   Basic computer skills.
     ๏ Properties of different OS: windows and unix-like
       systems.
     ๏ The internet.


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Topic 2

  Biological databases.
 •   How to deal with databases?
 •   Information retrieval from biological databases.
 •   Sequence databases.
     ๏   DNA
     ๏   Protein
 •   Genomic databases.




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Topic 3

  Sequence analysis
 •   Gene detection and genome annotation.
     ๏   Predictive methods using DNA sequences.
 •   Secondary structure prediction and analysis of protein
     sequences.
     ๏   Obtaining secondary structure from sequence.
     ๏   Predictive methods using protein sequences.
 •   Producing and analyzing sequence alignments.
     ๏   Pairwise sequence alignment and database searching.
     ๏   Multiple sequence alignments, patterns and profiles.
     ๏   Creation and analysis of protein multiple sequence
         alignments.
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Topic 4

  Comparative genomics.
 •   What is genomics?
 •   What do we learn from different genomes?
 •   Computational approaches in comparative genomics.




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Bonus topics

 DNA microarray and its analysis.
 Developmental tools: Perl.
 Systems biology.




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Qualification

  Mid-exam
 •   Open book
 •   30%

  Final-exam
 •   Open book
 •   30%

  Home work
 •   Send to me: chiu.weihsin@thu.edu.tw
 •   40%

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Contact me

 Office hour
 •   Every monday, 10:00~12:00 am

 Place
 •   LS133

 Phone
 •   32436

 E-Mail
 •   chiu.weihsin@thu.edu.tw

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