This book is an introduction to computational molecular biology, describes its most typical problems and offers effective algorithms for solving them. The book begins with an overview of the fundamental concepts of molecular biology (including the structure and functions of proteins and nucleic acids, mechanisms of molecular genetics), then the most important mathematical objects, such as graphs and strings, are introduced, and general information about algorithms is given. All of this sets the stage for understanding further sections of the book: sequence comparison (and database searches), DNA fragment assembly, physical DNA mapping, phylogenetic trees, gene rearrangement, macromolecule structure prediction, and DNA calculations. Each of these sections contains a discussion of biological prerequisites, definitions of key terms, a complete description of the mathematical or computer models used, as well as examples of the implementation of algorithms.