1st Edition

Introduction to Bioinformatics

By Anna Tramontano Copyright 2007
    192 Pages 68 B/W Illustrations
    by Chapman & Hall

    192 Pages
    by Chapman & Hall

    192 Pages 8 Color & 68 B/W Illustrations
    by Chapman & Hall

    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
    Structural Genomics
    But This Is Not All
    Useful Web Sites
    A Glossary, References, and Problems appear in each chapter.


    Anna Tramontano

    “… Overall, the book is well organized and clearly written. This book is a good mixture of theory and practical applications. … graduate and research students of biostatistics who want to pursue a career in experimental biology will enjoy this book. In addition, practitioners in cancer research and forensic science will find this book quite useful. I also recommend it for library purchase.”
    —Kuldeep Kumar (Bond University), Journal of the Royal Statistical Society

    "…Introduction to Bioinformatics serves a noble purpose … Tramontano’s added emphasis on proteomics should serve as an indication of a major current focus of bioinformatics and also to welcome Introduction to Bioinformatics into the canon of bioinformatics-related literature."
    —Eric D. Foster, University of Iowa, The American Statistician, August 2008

    "This book provides a nice summary of introductory topics in bioinformatics, suitable for higher-level undergraduates with some biological background looking to enter the field or masters-level graduate students. … the subject matter is informative and well written for an introductory book."
    International Statistical Review, 2008

    “By reading the book from cover to cover, the reader will acquire a sense of the richness of the field of bioinformatics.”
    —Jonathan Hodgson, Zentralblatt Math, Vol. 1115 (2007/17)