1. Algorithms for Biological Sequence Analysis
Kun-Mao Chao (趙坤茂)
Department of Computer Science and Information Engineering
National Taiwan University, Taiwan
Date: Feb. 22, 2011
WWW:

2. 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
Spring semester, 2011
9: :10 Tuesday, 107 CSIE Building
3 credits
Web site:

3. Coursework: Homework assignments and Class participation (10%)
Two midterm exams (70%; 35% each):
April 12, 2011 (tentatively)
May 24, 2011 (tentatively)
Oral presentation of selected papers (20%)

4. Outlines Part I: Sequence Homology Part II: Sequence Composition
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

5. 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]

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

7. 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

8. Milestones of Bioinformatics (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. Milestones of Bioinformatics (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. Milestones of Bioinformatics (cont’d)
Human Genome Project ( )
Mouse 2002
Rat 2004
Chimpanzee 2005
Completed Genomes

11. Chimpanzee Genome

12. The Primate Family Tree
Source: Nature

13. A Sequence Analysis Book Published by Springer in 2009 (ISBN 978-1848003194)
Sequence Comparison: Theory and Methods
by Kun-Mao Chao and Louxin Zhang