Introduction Bioinformatics

Guiding readers from the elucidation and analysis of a genomic sequence to the prediction of a protein structure and the identification of the molecular function, Introduction to Bioinformatics describes the rationale and limitations of the bioinformatics methods and tools that can help solve biological problems. Requiring only a limited mathematical and statistical background, the book shows how to efficiently apply these approaches to biological data and evaluate the resulting information. The author, an expert bioinformatics researcher, first addresses the ways of storing and retrieving the enormous amount of biological data produced every day and the methods of decrypting the information encoded by a genome. She then covers the tools that can detect and exploit the evolutionary and functional relationships among biological elements. Subsequent chapters illustrate how to predict the three-dimensional structure of a protein. The book concludes with a discussion of the future of bioinformatics. Even though the future will undoubtedly offer new tools for tackling problems, most of the fundamental aspects of bioinformatics will not change. This resource provides the essential information to understand bioinformatics methods, ultimately facilitating in the solution of biological problems.

The Data: Storage and Retrieval Basic Principles The Data Data Quality Data Representation Genome Sequence Analysis Basic Concepts Genome Sequencing Finding the Genes Statistical Methods to Search for Genes Comparative Genomics A Virtual Window on Genomes: The World Wide Web Protein Evolution Basic Concepts Molecular Evolution How to Align Two Similar Sequences Similarity Matrices Penalties for Insertions and Deletions The Alignment Algorithm Multiple Alignments Phylogenetic Trees Similarity Searches in Databases Basic Principles The Methods Amino Acid Sequence Analysis Basic Principles Search for Sequence Patterns Feature Extraction Secondary Structure: Part One Prediction of the Three-Dimensional Structure of a Protein Basic Principles The CASP Experiment Secondary Structure Prediction: Part Two Long-Range Contact Prediction Predicting Molecular Complexes: Docking Methods Homology Modeling Basic Principles The Steps of Comparative Modeling Accuracy of Homology Models Manual versus Automatic Models Practical Notes Summing Up Fold Recognition Methods Basic Principles Profile-Based Methods Threading Methods The Fold Library How Well Do These Methods Work? New Fold Modeling Basic Principles Estimating the Energy of a Protein Conformation Energy Minimization Molecular Dynamics The “Omics” Universe Basic Principles Transcriptomics Proteomics Interactomics Structural Genomics Pharmacogenomics But This Is Not All Useful Web Sites Index A Glossary, References, and Problems appear in each chapter.