Algorithms for Biological Sequence Analysis

1
Algorithms for Biological Sequence Analysis

• Kun-Mao Chao (???)
• Department of Computer Science and Information
  Engineering
• National Taiwan University, Taiwan
• Date September, 2008
• 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, 2008
• Wednesday 1320 1620, 107 CSIE Building.
• 3 credits
• Web site http//www.csie.ntu.edu.tw/kmchao/seq08
  fall

3
Coursework

• Homework assignments and Class participation
  (15)
• Two midterm exams (60 30 each)
• October 29, 2008 (tentatively)
• December 17, 2008 (tentatively)
• Oral presentation of selected papers (25)

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Outlines

• Part I Sequence Homology
• Introduction to genomes
• Dynamic programming strategy revisited
• Pairwise sequence alignment
• Multiple sequence alignment
• Chaining algorithms for genomic sequence analysis
• Suboptimal alignment
• Comparative genomics
• Hidden Markov models (the Viterbi algorithm et
  al.)
• Part II Sequence Composition
• Maximum-sum and maximum-density segments
• SNP and haplotype data analysis
• Genome annotation
• Other advanced topics

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A Brief History of Genetics

• 1859 Darwin publishes The Origin of Species
• 1865 Genes are particular factors
• 1871 Discovery of nucleic acid
• 1903 Chromosomes are hereditary units
• 1910 Genes lie on chromosomes
• 1913 Chromosomes are linear arrays of genes
• 1931 Recombination occurs by crossing over

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A Brief History of Genetics (contd)

• 1944 DNA is the genetic material
• 1945 A gene codes for protein
• 1951 First protein sequence
• 1953 DNA is a double helix
• 1961 Genetic code is triplet
• 1977 Eukaryotic genes are interrupted
• 1977 DNA can be sequenced
• 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 Bookto be published by Springer in Fall
2008 (ISBN 978-1848003194)

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