Catalog Description: Algorithms and probabilistic models that arise in various computational biology applications: suffix trees, suffix arrays, pattern matching, repeat finding, sequence alignment, phylogenetics, genome rearrangements, hidden Markov models, gene finding, motif finding, stochastic context free grammars, RNA secondary structure. There are no biology prerequisites for this course, but a strong quantitative background will be essential.

Units: 4

Prerequisites: COMPSCI 70 and COMPSCI 170; experience programming in a language such as C, C++, Java, or Python.

Formats:
Fall: 3.0 hours of lecture and 1.0 hours of discussion per week
Spring: 3.0 hours of lecture and 1.0 hours of discussion per week

Grading basis: letter

Final exam status: Written final exam conducted during the scheduled final exam period

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