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| Preface | |
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| Introduction and Biological Databases | |
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| Introduction | |
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| What Is Bioinformatics? | |
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| Goal | |
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| Scope | |
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| Applications | |
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| Limitations | |
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| New Themes | |
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| Further Reading | |
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| Introduction to Biological Databases | |
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| What Is a Database? | |
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| Types of Databases | |
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| Biological Databases | |
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| Pitfalls of Biological Databases | |
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| Information Retrieval from Biological Databases | |
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| Summary | |
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| Further Reading | |
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| Sequence Alignment | |
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| Pairwise Sequence Alignment | |
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| Evolutionary Basis | |
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| Sequence Homology versus Sequence Similarity | |
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| Sequence Similarity versus Sequence Identity | |
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| Methods | |
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| Scoring Matrices | |
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| Statistical Significance of Sequence Alignment | |
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| Summary | |
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| Further Reading | |
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| Database Similarity Searching | |
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| Unique Requirements of Database Searching | |
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| Heuristic Database Searching | |
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| Basic Local Alignment Search Tool (BLAST) | |
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| FASTA | |
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| Comparison of FASTA and BLAST | |
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| Database Searching with the Smith-Waterman Method | |
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| Summary | |
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| Further Reading | |
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| Multiple Sequence Alignment | |
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| Scoring Function | |
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| Exhaustive Algorithms | |
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| Heuristic Algorithms | |
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| Practical Issues | |
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| Summary | |
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| Further Reading | |
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| Profiles and Hidden Markov Models | |
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| Position-Specific Scoring Matrices | |
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| Profiles | |
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| Markov Model and Hidden Markov Model | |
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| Summary | |
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| Further Reading | |
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| Protein Motifs and Domain Prediction | |
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| Identification of Motifs and Domains in Multiple Sequence Alignment | |
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| Motif and Domain Databases Using Regular Expressions | |
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| Motif and Domain Databases Using Statistical Models | |
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| Protein Family Databases | |
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| Motif Discovery in Unaligned Sequences | |
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| Sequence Logos | |
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| Summary | |
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| Further Reading | |
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| Gene and Promoter Prediction | |
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| Gene Prediction | |
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| Categories of Gene Prediction Programs | |
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| Gene Prediction in Prokaryotes | |
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| Gene Prediction in Eukaryotes | |
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| Summary | |
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| Further Reading | |
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| Promoter and Regulatory Element Prediction | |
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| Promoter and Regulatory Elements in Prokaryotes | |
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| Promoter and Regulatory Elements in Eukaryotes | |
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| Prediction Algorithms | |
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| Summary | |
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| Further Reading | |
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| Molecular Phylogenetics | |
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| Phylogenetics Basics | |
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| Molecular Evolution and Molecular Phylogenetics | |
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| Terminology | |
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| Gene Phylogeny versus Species Phylogeny | |
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| Forms of Tree Representation | |
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| Why Finding a True Tree Is Difficult | |
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| Procedure | |
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| Summary | |
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| Further Reading | |
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| Phylogenetic Tree Construction Methods and Programs | |
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| Distance-Based Methods | |
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| Character-Based Methods | |
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| Phylogenetic Tree Evaluation | |
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| Phylogenetic Programs | |
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| Summary | |
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| Further Reading | |
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| Structural Bioinformatics | |
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| Protein Structure Basics | |
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| Amino Acids | |
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| Peptide Formation | |
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| Dihedral Angles | |
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| Hierarchy | |
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| Secondary Structures | |
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| Tertiary Structures | |
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| Determination of Protein Three-Dimensional Structure | |
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| Protein Structure Database | |
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| Summary | |
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| Further Reading | |
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| Protein Structure Visualization, Comparison, and Classification | |
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| Protein Structural Visualization | |
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| Protein Structure Comparison | |
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| Protein Structure Classification | |
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| Summary | |
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| Further Reading | |
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| Protein Secondary Structure Prediction | |
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| Secondary Structure Prediction for Globular Proteins | |
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| Secondary Structure Prediction for Transmembrane Proteins | |
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| Coiled Coil Prediction | |
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| Summary | |
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| Further Reading | |
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| Protein Tertiary Structure Prediction | |
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| Methods | |
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| Homology Modeling | |
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| Threading and Fold Recognition | |
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| Ab Initio Protein Structural Prediction | |
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| CASP | |
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| Summary | |
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| Further Reading | |
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| RNA Structure Prediction | |
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| Introduction | |
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| Types of RNA Structures | |
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| RNA Secondary Structure Prediction Methods | |
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| Ab Initio Approach | |
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| Comparative Approach | |
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| Performance Evaluation | |
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| Summary | |
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| Further Reading | |
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| Genomics and Proteomics | |
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| Genome Mapping, Assembly, and Comparison | |
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| Genome Mapping | |
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| Genome Sequencing | |
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| Genome Sequence Assembly | |
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| Genome Annotation | |
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| Comparative Genomics | |
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| Summary | |
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| Further Reading | |
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| Functional Genomics | |
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| Sequence-Based Approaches | |
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| Microarray-Based Approaches | |
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| Comparison of SAGE and DNA Microarrays | |
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| Summary | |
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| Further Reading | |
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| Proteomics | |
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| Technology of Protein Expression Analysis | |
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| Posttranslational Modification | |
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| Protein Sorting | |
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| Protein-Protein Interactions | |
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| Summary | |
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| Further Reading | |
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| Appendix | |
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| Practical Exercises | |
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| Glossary | |
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| Index | |