BME205, Fall 2011, Section 01: Pairwise Alignment

Chapter 6: Jones and Pevzner (6.6 - 6.10 especially)

Chapter 2: Durbin and Eddy (all of Chapter 2)

We will be covering substitution matrices, then global alignment with linear gap cost, then consider local alignments and finally consider Affine Gap costs.  Pay special attention to the graphical models presented in JP.