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.
Biography
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)
