ABSTRACT
Chapter 1 provides an introduction to HMMs and related Profile methods. This chapter presents the problem of standard pairwise algorithms such as BLAST or FASTA, and then demonstrates ways in which the various profile methods provide a better solution. This chapter provides the basic understanding of what a Hidden Markov Model really is, in terms of bioinformatics, and why they are used instead of other methods. We will cover some of the background about how HMMs came to be used for biological sequence analysis, but will not spend too much time on the underlying mathematical theory. For those who are interested in the underlying basis of Hidden Markov Models and their use in bioinformatics, I recommend the other excellent books on the subject, particularly “Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids” by Durbin, Eddy, Krogh and Mitchison, and “Hidden Markov Models of bioinformatics” by Koski. Particularly for the more mathematically inclined or for those interested in developing new algorithms, these books will provide an understanding of the equations and calculations that will not be covered here.
