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.

Contents:

• Molecular Biology for the Practical Bioinformatician
• Strategy and Planning of Bioinformatics Experiments
• Data Mining Techniques for the Practical Bioinformatician
• Techniques for Recognition of Translation Initiation Sites
• How Neural Networks Find Promoters Using Recognition of Micro-Structural Promoter Components
• Neural-Statistical Model of TATA-Box Motifs in Eukaryotes
• Tuning the Dragon Promoter Finder System for Human Promoter Recognition
• RNA Secondary Structure Prediction
• Protein Localization Prediction
• Homology Search Methods
• Analysis of Phylogeny: A Case Study on Saururaceae
• Functional Annotation and Protein Families: From Theory to Practice
• Discovering Protein–Protein Interactions
• Techniques for Analysis of Gene Expression
• Genome-Wide cDNA Oligo Probe Design and Its Applications in Schizosaccharomyces Pombe
• Mining New Motifs from cDNA Sequence Data
• Technologies for Biological Data Integration
• Construction of Biological Databases: A Case Study on the Protein Phosphatase DataBase (PPDB)
• A Family Classification Approach to Functional Annotation of Proteins
• Informatics for Efficient EST-Based Gene Discovery in Normalized and Subtracted cDNA Libraries