Unfortunately, we have yet to find a single text that covers all of the topics discussed in this course in sufficient detail to serve as a course textbook. The following three texts provide most of the background and algorithmic details for the material covered in the course. Of course it is not realistic to require students to purchase three books for only a 3 unit course, so we have purchased copies of these texts and made them available for limited-time checkout at the Reserved Book Desk in the UCSF library. However, if you plan to be involved in algorithm design and implementation beyond just this course, we highly recommend all of these texts, especially the one by Cormen, Leiserson, and Rivest.
- T.H. Cormen, C.E. Leiserson, and R.L. Rivest, "Introduction to Algorithms," 2nd edition, MIT press, 2001. (~$50 paperback)
- R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids," Cambridge University Press, 1999. ($35 paperback)
- W.H. Press, S.A. Teukolsky, W.T. Vetterling, and B.P. Flannery, "Numerical Recipes in C - The Art of Scientific Computing," 2nd edition, Cambridge University Press, 1992. (~$30 used)
(If you're interested in buying a used edition of any of these books, be sure to check the bookstores around the UC Berkeley campus.)