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Algorithms for Biological Sequence Analysis

This course focuses on algorithmic problems related to biological sequence analysis, with an emphasis on genomic sequences. Topics include dynamic programming, sequence alignment, hidden Markov models, comparative genomics, and more.

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Algorithms for Biological Sequence Analysis

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  1. Algorithms for Biological Sequence Analysis Kun-Mao Chao (趙坤茂) Department of Computer Science and Information Engineering National Taiwan University, Taiwan E-mail: kmchao@csie.ntu.edu.tw WWW: http://www.csie.ntu.edu.tw/~kmchao

  2. About this course • Course: Algorithms for biological sequence analysis • We will be focused on the sequence-related algorithmic problems. Genomic sequences are our main target. • Fall semester, 2005 • Wednesday 14:20 – 17:20, 111 CSIE Building. • 3 credits • Web site: http://www.csie.ntu.edu.tw/~kmchao/seq05fall

  3. Coursework: • Programming assignments and Class participation (30%) • One exam (40%) • Oral presentation of selected papers (30%)

  4. Outlines • Introduction to genomes • Dynamic programming strategy revisited • Maximum-sum and maximum-density segments • Pairwise sequence alignment • Multiple sequence alignment • Suboptimal alignment • Hidden Markov models (the Viterbi algorithm et al.) • Comparative genomics • Phylogenetic trees • SNP and haplotype data analysis • Genome annotation • Other advanced topics

  5. 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

  6. A Brief History of Genetics (cont’d) • 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

  7. Bioinformatics Milestones • 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

  8. Bioinformatics Milestones (cont’d) • 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

  9. Bioinformatics Milestones (cont’d) • 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

  10. New Bioinformatics Age • Human Genome Project (1990-2003) • Mouse 2002 • Rat 2004 • Chimpanzee 2005 • Completed Genomes

  11. Chimpanzee Genome

  12. The Primate Family Tree

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