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Much knowledge of biological systems is acquired by making comparisons with known systems. Several computational methods, including Markov models, HMMs and dynamic programming can be used in making these comparisons. Technical aspects of these methods and their application to biological problems will be discussed. A sound understanding of BIOSCI 359 or BIOINF 301 or equivalent is assumed. Students lacking this background must take BIOINF 701 as a corequisite.