CSE 527, Winter 2000
Computational Biology
Martin Tompa

Tuesdays & Thursdays, 12:00-1:20
Loew 102

Course Information

Class Messages (Last message: .)


Lecture Date Topic Notes
All notes below as one technical report pdf ps
Table of Contents pdf ps
1 1/4 Basics of Molecular Biology Michael Gates pdf ps LaTeX
2 1/6 Basics of Molecular Biology (continued) Tory McGrath pdf ps LaTeX
3 1/11 Introduction to Sequence Similarity Martin Tompa pdf ps
4 1/13 Alignment by Dynamic Programming Martin Tompa pdf ps
5 1/18 Local Alignment, and Gap Penalties Martin Tompa pdf ps
6 1/20 Multiple Sequence Alignment Martin Tompa pdf ps
7 1/25 Finding Instances of Known Sites Elisabeth Rosenthal pdf ps
8 1/27 Relative Entropy Anne-Louise Leutenegger pdf ps
9 2/1 Relative Entropy and Binding Energy Neil Spring pdf ps
10 2/8 Finding Instances of Unknown Sites Dylan Chivian pdf ps
11 2/10 Correlation of Positions in Sequences Tammy Williams pdf ps
12 2/15 Maximum Subsequence Problem Mathieu Blanchette pdf ps
13 2/17 Markov Chains Jonathan Schaefer pdf ps
14 2/22 Using Interpolated Context Models to Find Genes Gretta Bartels pdf ps
15 2/24 Start Codon Prediction Mingzhou Song pdf ps
16 2/29 RNA Secondary Structure Prediction Matthew Cary pdf ps
17 3/2 RNA Secondary Structure Prediction (continued) Don Patterson pdf ps
18 3/7 Speeding Up Internal Loop Computations Kellie Plow pdf ps

LaTeX template for lecture notes

Project Ideas (Last update: .)

Homework: pdf, ps

Reviews of Tools and Databases

Relevant Biology Links (Last update: .)

Introducing Algorithms to Nonspecialists (Word document, written retrospectively by a nonspecialist)

CSE 590BI Webs (earlier version of CSE 527): Winter 1996, Winter 1998

About file formats

Course materials above are provided in several formats:
Ordinary Web pages.
Use the free Adobe Acrobat viewer.
Use the free Ghostview/Ghostscript PostScript viewer.
The LaTeX source from which the pdf and ps were produced, for use as examples by the notetakers.

owner-cse527@cs.washington.edu (Last Update: )
visits since 1/1/00.