This book is written mainly for biologists who want to understand the methods of sequence and structure analysis. I strongly believe that a person using a computer program should understand how it works. Accordingly, one of my main objectives is to help biologists appreciate the underlying algorithms used and assumptions made, as well as limitations of the methods used and strategies for their use. To this end, I have tried to avoid complex formulas and notations and to give instead simple numerical examples whenever possible. I hope that the book will also be of interest to computational biologists who want to learn a little more about the biological questions related to the field of bioin-formatics. This book is intended to be a laboratory reference text, as well as a textbook for a course in bioinformatics, rather than a user guide for a specific set of sequence analysis programs.