| Date | Topic | Text Readings
|
| T 1/8 | Course Intro, Biological Problems in Need of Solutions
|
| R 1/10 | Algorithms as Possible Solutions | A Chapter 2 |
| T 1/15 |
Algorithmic Techniques and
Biological Strings (DNA Replication, Transcription) | B 19-22 (Begining of Chapter 2 up to section "Protein"), or A Chapter 3 |
| R 1/17 | Biological Strings (Translation);
Problem Solving;
Intro to Perl
| B 22-27 (Chapter 2 "Protein" up to "Mutation"), 35-37 (Chapter 2 "Genomes and Genes" up to "Pseudogenes"); P Chapter 3 |
| T 1/22 | Regular Expressions and Patterns in Biology; Problem Solving |
A 83-91, P Chapter 4 |
| R 1/24 | No Class |
| T 1/29 | Regular expressions in Biology and
Computer Science | P Chapter 4
|
| R 1/31 | Practice with Regular Expressions |
| T 2/5 | Exam I |
| R 2/7 | Perl: Subroutines and Files | P Chapters 7 and 8 |
| T 2/12 | Global vs. Local Sequence Alignments | B 3 (What is Blast?), 32-33 (Homology, Phylogeny & Trees and The Tree of Life), 40-53 (All of Chapter 3) |
| R 2/14 | Dynamic Computation Algorithms (example perl files)
and Blast | A Chapter 6, sections 6.1, 6.2, 6.4, 6.6, 6.8 |
| T 2/19 | Alignment Algorithms, including BLAST + Worksheet |
B Chapter 5, also A chapter 9 especially 9.6-9.8 |
| R 2/21 | How BLAST Works (continued) |
B Chapter 6, Chapter 7 through "The Expect of an HSP" |
| T 2/26 | Ab Initio Gene Calling | A 197-200 (6.12) GLIMMER Paper, A Chapter 11 (Background on Hidden Markov Models and the decoding problem) |
| R 2/28 | Project 1 Presentations |
| T 3/4 | Project 1 Presentations |
| T 3/18 | Exam II |
| T 3/18 | Research for Project 2 |
| T 3/25 | Beyond BLAST analysis of protein sequences |
Predicting protein function from sequence and structural data |
| R 3/27 | Introduction to Databases |
| T 4/1 | Hidden Markov Models | A Chapter 11 |
R 4/3 | Work on Project 2 |
| T 4/8 | Project 2 Presentations |
| R 4/10 | Exam III | Study Guide |