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1 Introduction/Sequence Comparison and Dynamic Programming
2 Multiple Sequence Alignments I
3 Multiple Sequence Alignments II Homework 1 handed out
4 Phylogenetic Analysis
5 Literature Discussion
6 Genome Sequencing and DNA Sequence Analysis Homework 1 due
7 DNA Sequence Comparison and Alignment
8 DNA Motif Modeling and Discovery Homework 2 handed out
9 Markov and Hidden Markov Models for DNA Sequences
10 DNA Sequence Evolution
11 RNA Secondary Structure Prediction Homework 2 due
12 Literature Discussion on Predicting the Functions of DNA/RNA Sequences
13 Midterm Exam – in class – Protein and DNA Sequence Analysis
14 Protein Secondary Structure Prediction
15 Introduction to Protein Structure and Classification
16 Comparing Protein Structures

Molecular Modeling: Methods and Applications
17 Using Computational Methods to Analyze, Predict, and Design Protein Sequences and Structures

Solving Structures using X-ray Crystallographpy and NMR
18 Solving Structures using X-ray Crystallographpy and NMR (cont.)

Homology Modeling
Homework 3 handed out
19 Methods for Protein Structure Prediction: Homology Modeling and Fold Recognition
20 Threading and ab initio Structure Prediction

Computational Protein Design
Homework 3 due
21 Introduction to Systems Biology Homework 4 handed out
22 Feedback Systems and Coupled Differential Equations
23 DNA Microarrays and Clustering
24 Literature Discussion on DNA Microarrays and Clustering Homework 4 due
(a day after Lec #24)
25 Computational Annotation of the Proteome
26 Literature Discussion on Computational Annotation of the Proteome