Web site: http://www.csie.ntu.edu.tw/~kmchao/seq04spr

Prerequisites:
Some basic knowledge on algorithm development and program design is required. Background in bioinformatics and computational biology is welcome but not required for taking this course.Outline:
1. Introduction to sequence analysis
2. Dynamic programming strategy revisited
3. Maximum-sum and maximum-density segments
4. Pairwise sequence alignment
5. Multiple sequence alignment
6. Suboptimal alignment
7. Hidden Markov models (the Viterbi algorithm et al.)
8. Comparative genomics
9. Phylogenetic trees
10. SNP and haplotype data analysis
11. Genome annotation
12. Other advanced topics

References:
1.Class notes
2.Related journal and conference papers
3.Introduction to Computational Molecular Biology, by Joao Carlos Setubal and Joao Meidanis (1996)
4.Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, by Dan Gusfield (1997)
5.Biological Sequence Analysis, by Richard Durbin et al. (1998)
6.Computational Molecular Biology: An Algorithmic Approach, by Pavel Pevzner (2000)

Coursework:Programming assignments (25%)Midterm exam (40%)Final project (Oral presentation of selected papers) (30%)Class participation (5%)