Contents

Chapters in this book

1. Frontmatter i
2. Contents vii
3. Preface xi
4. PART 1. Preliminaries
5. Chapter One. Introduction to Probability and Random Variables 3
6. Chapter Two. Introduction to Information Theory 45
7. Chapter Three. Nonnegative Matrices 71
8. PART 2. Hidden Markov Processes
9. Chapter Four. Markov Processes 101
10. Chapter Five. Introduction to Large Deviation Theory 129
11. Chapter Six. Hidden Markov Processes: Basic Properties 164
12. Chapter Seven. Hidden Markov Processes: The Complete Realization Problem 177
13. PART 3. Applications to Biology
14. Chapter Eight. Some Applications to Computational Biology 225
15. Chapter Nine. BLAST Theory 255
16. Bibliography 273
17. Index 285
18. Backmatter 288