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  CSE 527Au '07:  Computational Biology
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Lecture Slides
 1  : Introduction; Bio Basics (1-up4-up)
 2-3: Alignment; DNA Replication (1-up4-up)
 4-5: BLAST, Scoring; Sequencing (1-up4-up)
 6-7: MLE & EM; Gene Expression (1-up4-up)
         EM Example (.xls)
 8-9: Motifs; Gene Regulation (1-up4-up)
 12-13: HMMs (1-up4-up)
 15-16: Genes & Splicing (1-up4-up)
 17-18: RNA Folding; RNA Function (1-up4-up)
 18-20: RNA Motifs, Discovery, & Search (1-up4-up)
Lecture Notes
 0. (All of last year's notes)
 1. Overview
 2. More Bio Overview
 3. Global Alignment
 4. Local Alignment; BLAST
 5. Blast Statistics
 6. DNA Replication; MLE
 7. MLE & EM
 8. TF Binding; Weight Matrices
 9. MEME
 15. Pfam; Genes & Splicing
 16. More Gene Finding
 17. RNA Roles & Structure
 19. CMs II: Search
 20. CMs III: CMfinder
 NCBI Science Primer
 NHGRI Talking Glossary
 ORNL Genome Glossary
 A Molecular Biology Glossary

Lecture:  EEB 026 (schematic) MW 12:00- 1:20 
Office Hours Phone
Instructor:  Larry Ruzzo, ruzzo at cs  F 12:00- 1:00  CSE 554  (206) 543-6298

Course Email: Use this list to ask and/or answer questions about homework, lectures, etc. The instructor and TA are subscribed to this list. All messages are automatically archived.  Questions not of general interest may be directed to the instructor: ruzzo at cs. You can (and perhaps should) change your subscription options.

Catalog Description: Introduces computational methods for understanding biological systems at the molecular level. Problem areas such as mapping and sequencing, sequence analysis, structure prediction, phylogenic inference, regulatory analysis. Techniques such as dynamic programming, Markov models, expectation-maximization, local search. Prerequisite: graduate standing in biological, computer, mathematical or statistical science, or permission of instructor.

Prerequisite: None.

Credits: 3

Textbook: Richard Durbin, Sean R. Eddy, Anders Krogh and Graeme Mitchison, Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids, Cambridge, 1998. (U. Book Store, Amazon) Errata.

References: See Schedule & Reading.

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