Introduction to Bioinformatics (Paperback)

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.