Computer scientists have increasingly been enlisted as “bioinformaticians” to assist molecular biologists in their research. This book is a practical introduction to bioinformatics for these computer scientists. The chapters are in-depth discussions by expert bioinformaticians on both general techniques and specific approaches to a range of selected bioinformatics problems. The book is organized into clusters of chapters on the following topics:

• Overview of modern molecular biology and a broad spectrum of techniques from computer science — data mining, machine learning, mathematical modeling, sequence alignment, data integration, workflow development, etc.

• In-depth discussion of computational recognition of functional and regulatory sites in DNA sequences.

• Incisive discussion of computational prediction of secondary structure of RNA sequences.

• Overview of computational prediction of protein cellular localization, and selected discussions of inference of protein function.

• Overview of methods for discovering protein–protein interactions.

• Detailed discussion of approaches to gene expression analysis for the diagnosis of diseases, the treatment of diseases, and the understanding of gene functions.

• Case studies on analysis of phylogenies, functional annotation of proteins, construction of purpose-built integrated biological databases, and development of workflows underlying the large-scale-effort gene discovery.