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| Introduction | |
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| Biology in the Computer Age | |
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| How Is Computing Changing Biology? | |
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| Isn't Bioinformatics Just About Building Databases? | |
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| What Does Informatics Mean to Biologists? | |
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| What Challenges Does Biology Offer Computer Scientists? | |
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| What Skills Should a Bioinformatician Have? | |
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| Why Should Biologists Use Computers? | |
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| How Can I Configure a PC to Do Bioinformatics Research? | |
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| What Information and Software Are Available? | |
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| Can I Learn a Programming Language Without Classes? | |
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| How Can I Use Web Information? | |
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| How Do I Understand Sequence Alignment Data? | |
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| How Do I Write a Program to Align Two Biological Sequences? | |
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| How Do I Predict Protein Structure from Sequence? | |
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| What Questions Can Bioinformatics Answer? | |
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| Computational Approaches to Biological Questions | |
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| Molecular Biology's Central Dogma | |
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| What Biologists Model | |
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| Why Biologists Model | |
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| Computational Methods Covered in This Book | |
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| A Computational Biology Experiment | |
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| The Bioinformatics Workstation | |
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| Setting Up Your Workstation | |
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| Working on a Unix system | |
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| Setting Up a Linux Workstation | |
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| How to Get Software Working | |
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| What Software Is Needed? | |
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| Files and Directories in Unix | |
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| Filesystem Basics | |
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| Commands for Working with Directories and Files | |
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| Working in a Multiuser Environment | |
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| Working on a Unix System | |
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| The Unix Shell | |
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| Issuing Commands on a Unix System | |
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| Viewing and Editing Files | |
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| Transformations and Filters | |
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| File Statistics and Comparisons | |
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| The Language of Regular Expressions | |
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| Unix Shell Scripts | |
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| Communicating with Other Computers | |
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| Playing Nicely with Others in a Shared Environment | |
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| Tools For Bioinformatics | |
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| Biological Research on the Web | |
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| Using Search Engines | |
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| Finding Scientific Articles | |
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| The Public Biological Databases | |
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| Searching Biological Databases | |
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| Depositing Data into the Public Databases | |
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| Finding Software | |
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| Judging the Quality of Information | |
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| Sequence Analysis, Pairwise Alignment, and Database Searching | |
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| Chemical Composition of Biomolecules | |
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| Composition of DNA and RNA | |
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| Watson and Crick Solve the Structure of DNA | |
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| Development of DNA Sequencing Methods | |
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| Genefinders and Feature Detection in DNA | |
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| DNA Translation | |
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| Pairwise Sequence Comparison | |
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| Sequence Queries Against Biological Databases | |
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| Multifunctional Tools for Sequence Analysis | |
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| Multiple Sequence Alignments, Trees, and Profiles | |
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| The Morphological to the Molecular | |
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| Multiple Sequence Alignment | |
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| Phylogenetic Analysis | |
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| Profiles and Motifs | |
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| Visualizing Protein Structures and Computing Structural Properties | |
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| A Word About Protein Structure Data | |
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| The Chemistry of Proteins | |
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| Web-Based Protein Structure Tools | |
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| Structure Visualization | |
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| Structure Classification | |
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| Structural Alignment | |
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| Structure Analysis | |
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| Solvent Accessibility and Interactions | |
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| Computing Physicochemical Properties | |
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| Structure Optimization | |
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| Protein Resource Databa | |