Introduction
DNA, RNA, proteins, the central dogma in molecular biology, splicing, gene structure

Sequence Alignments
Homology, alignments and dynamic programming
Local alignment, heuristic local alignment and BLAST
Advanced alignment techniques: linear space, affine gaps, banded linear time alignments, time warping

Hidden Markov Models
Markov chains and hidden Markov models
The Viterbi algorithm
Parameter estimation for HMMs
Connection between pair HMMs and alignments

Applications of alignments and HMMs: Analysis of a genome
The human genome: chromosomes, repeats, genes, and SNPs
Gene Recognition
Suffix Trees
Comparative genomics, efficient alignment algorithms
Cross-species comparison-based gene recognition

Multiple sequence alignments
Definition, multidimensional dynamic programming
Progressive alignment, CLUSTALW
Expectation maximization, Gibbs sampling
Applications: microarrays and gene regulation

Sequencing of a Genome
Sequencing methods
Computational assembly of a genome

Conclusion
Current active areas and open problems in computational genomics

Problem Set Schedule:

• Problem Set 1: handed out Jan 15, due Jan 29
• Problem Set 2: handed out Jan 29, due Feb 12
• Problem Set 3: handed out Feb 12, due Feb 26
• Problem Set 4: handed out Feb 26, due Mar 11