This is an introduction to the computational approaches that play a critical role in the emerging branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches to the subject and of the potential and limitations of computational and experimental approaches to genome analysis. Key topics covered in this textbook are: the completed and ongoing genome sequencing projects; databases that store and organize genomic data, with their unique advantages and pitfalls; principles and methods of genome analysis and annotation; ways to automate the searches and increase search sensitivity while minimizing the error rate; the first lessons from the Human Genome Project; the contribution of comparative genomics to the understanding of hereditary diseases and cancer; fundamental and practical applications of comparative genomics; the use of complete genomes for evolutionary analysis; the application of comparative genomics for identification of potential drug targets in microbial genomes; and problems for further study, which are designed to be solved by using methods available through the World Wide Web.