The second edition of this book has been thoroughly updated and enhanced. The text continues to offer the most broad-based introduction to this explosive new discipline, combining theoretical context with practical applications. The first third of this book covers bioinformatics, a new field at the interface of the ongoing revolutions in molecular biology and computers. A focus of this new discipline is the use of computer databases and computer algorithms to study proteins and genes, including sequence alignment, database searches, and phylogeny. The middle third of this book focuses on functional genomics including approaches such as gene expression profiling and proteomics that are used to study cellular function. The last third of the book is on genomics which is the study of the collection of DNA that comprises an organism, using the tools of bioinformatics. This portion of the book spans the tree of life from viruses to prokaryotes and eukaryotes, including a description of the human genome in health and disease.