ABSTRACT
Chapter 2 continues and expands the instruction on HMMs and the various states that may be found in an HMM. Chapter 2 introduces the various models, such as the ‘Plan 7’ model, local versus global scoring, and the maximum entropy model. While this book will primarily discuss the use of HMMs for the discovery of protein family homology, we will cover what other types of applications HMMs have in the field of biology in chapter 8.
