This course is an interdisciplinary introduction to computational methods used to solve important problems in DNA and protein sequence and structure analysis. The course focuses on algorithms, but includes material to provide the necessary biological background for science and engineering students. Algorithms to be covered include dynamic programming for sequence alignment, such as Smith-Waterman, FASTA, and BLAST; hidden Markov models, such as the forward, Viterbi, and expectation maximization algorithms; and a range of gene-finding algorithms. The course also covers basic concepts related to phylogenic tree construction.

Prerequisites: Familiarity with probability and statistics; working knowledge of a programming language, a course in molecular biology, a course in cell biology or biochemistry, and a basic course in algorithms desiggn is highly recommended.