This is an archived course. A more recent version may be available at ocw.mit.edu.

Calendar

LEC # TOPICS KEY DATES
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