Algorithms for Biological Sequence Analysis

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Algorithms for Biological Sequence Analysis

• Kun-Mao Chao (???)
• Department of Computer Science and Information
  Engineering
• National Taiwan University, Taiwan
• Date September 14, 2009
• WWW http//www.csie.ntu.edu.tw/kmchao

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About this course

• Course Algorithms for biological sequence
  analysis
• Some basic knowledge on algorithm development and
  program design is required.
• We will be focused on the sequence-related
  algorithmic problems. Genomic sequences are our
  main target.
• The oldest language
• The largest program
• Fall semester, 2009
• 1320 1620 Monday, 107 CSIE Building.
• 3 credits
• Web site http//www.csie.ntu.edu.tw/kmchao/seq09
  fall

3
Coursework

• Homework assignments and Class participation
  (15)
• Two midterm exams (60 30 each)
• October 26, 2009 (tentatively)
• December 7, 2009 (tentatively)
• Oral presentation of selected papers (25)

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Outlines

• Part I Sequence Homology
• Introduction to basic algorithmic strategies
• Pairwise sequence alignment
• Multiple sequence alignment
• Chaining algorithms for genomic sequence analysis
• Suboptimal alignment
• Comparative genomics
• Compressed / constrained sequence comparison
• Hidden Markov models (the Viterbi algorithm et
  al.)
• Part II Sequence Composition
• Maximum-sum and maximum-density segments
• SNP and haplotype data analysis
• Approximate gapped palindrome
• Genome annotation
• Other advanced topics

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A Brief History of Genetics

• 1859 Charles Darwin published The Origin of
  Species.
• 1865 Genes are particular factors. Gregor
  Mendel
• 1869 Discovery of nucleic acid Friedrich
  Miescher
• 1903 Chromosomes are hereditary units. Walter
  Sutton
• 1910 Genes lie on chromosomes. Thomas Hunt
  Morgan
• 1913 Chromosomes are linear arrays of genes.
  Alfred Sturtevant

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A Brief History of Genetics (contd)

• 1931 Recombination occurs by crossing over.
  Harriet Creighton and Barbara McClintock
• 1944 DNA is the genetic material. Oswald Avery,
  Colin McLeod and Maclyn McCarty
• 1953 DNA is a double helix. James Watson and
  Francis Crick
• 1961-1967 Genetic code is triplet. Marshall
  Nirenberg, Har Gobind Khorana, Sydney Brenner
  Francis Crick
• 1977 DNA was sequenced for the first time. Fred
  Sanger, Walter Gilbert, and Allan Maxam
• 21th Century Many genomes completely sequenced

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Milestones of Bioinformatics

• 1962 Pauling's theory of molecular evolution
• 1965 Margaret Dayhoff's Atlas of Protein
  Sequences
• 1970 Needleman-Wunsch algorithm
• 1977 DNA sequencing and software to analyze it
  (Staden)
• 1981 Smith-Waterman algorithm developed
• 1981 The concept of a sequence motif (Doolittle)
• 1982 GenBank Release 3 made public
• 1982 Phage lambda genome sequenced

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Milestones of Bioinformatics (contd)

• 1983 Sequence database searching algorithm
  (Wilbur-Lipman)
• 1985 FASTP/FASTN fast sequence similarity
  searching
• 1988 National Center for Biotechnology
  Information (NCBI) created at NIH/NLM
• 1988 EMBnet network for database distribution
• 1990 BLAST fast sequence similarity searching
• 1991 EST expressed sequence tag sequencing
• 1993 Sanger Centre, Hinxton, UK
• 1994 EMBL European Bioinformatics Institute,
  Hinxton, UK

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Milestones of Bioinformatics (contd)

• 1995 First bacterial genomes completely sequenced
• 1996 Yeast genome completely sequenced
• 1997 PSI-BLAST
• 1998 Worm (multicellular) genome completely
  sequenced
• 1999 Fly genome completely sequenced

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Milestones of Bioinformatics (contd)

• Human Genome Project (1990-2003)
• Mouse 2002
• Rat 2004
• Chimpanzee 2005
• Completed Genomes

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Chimpanzee Genome
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The Primate Family Tree
Source Nature
13
A New BookPublished by Springer in 2009 (ISBN
978-1848003194)

• Sequence Comparison Theory and Methods
• by Kun-Mao Chao and Louxin Zhang