: Mon 1:20 PM – 4:05 PM

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CSIM-G2



— Special Topics on Bioinformatics 2003 Spring



: Mon 1:20 PM – 4:05 PM



:



(http://www.cs.pu.edu.tw/~yawlin)



:



412



:



417 (



)

Office Hours: Mon 8:20 – 11:59 AM

: 2632-8001 ext 13403

Bioinformatics is an interdisciplinary field that uses computational approaches to answer biological and biochemical questions. This course is designed to discuss algorithms for some important computational problems in Molecular Biology, especially in analyzing andclassification of genomes, genes, gene products/

proteins, andfunctions. We shall study exact algorithms for those problems which can be solvedefficiently, as well as complexity, approximation algorithms andheuristics for the more difficult problems. We shall concentrate on discrete realistic models for the biological problems. Many biological examples will be presented.

:

(1) Dan Gusfiled, Algorithms on Strings, Trees, and Sequences — Computter Science and Computational Biology, Cambridge University Press, 1997.

(2) Pavel A. Pevzner, Computational Molecular Biology — An Algorithmic Approach, MIT Press, 2000.

(3) R. Durbin, S. Eddy, A. Krough, and G. Mitchison. Biological Sequence Analysis: Proba- bilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998.

Æ

: Grades will be assigned based on the following formula, with cut-offs determined by my opinion of students on the boundary.

Two Homeworks — 30%

Midterm Take Home — 30%

Final Take Home Exam — 40%



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Note

---- ---- ---- ----

02/17 Introductory Concepts

02/24 Exact String Matching G2-4

03/03 Least Common Ancestor G8

03/10 Suffix Trees 1 G5

03/17 Suffix Trees 2 G6

03/24 Applications of Suffix Trees G7-9 03/31

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04/07 Sequence Alignment G11-13,D2

04/14

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Midterm In

04/21 Multiple Sequence Alignment G14,P7,D6

04/28 Hidden Markov Models D3

05/05 Phylogeny 1 D7

05/12 Phylogeny 2 D8

05/19 Genome Rearrangement P10

05/26 Structural Bioinformatics 1 06/02 Structural Bioinformatics 2

06/09

¡ª©

Final In

Providence University Yaw-Ling Lin

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