Audience for This Book
Structure of This Book
Our Approach to Bioinformatics
URLs Referenced in This Book
Conventions Used in This Book
Comments and Questions
Acknowledgments
I: Introduction
1. Biology in the Computer Age
1.1 How Is Computing Changing Biology?
1.2 Isn't Bioinformatics Just About Building Databases?
1.3 What Does Informatics Mean to Biologists?
1.4 What Challenges Does Biology Offer Computer Scientists?
1.5 What Skills Should a Bioinformatician Have?
1.6 Why Should Biologists Use Computers?
1.7 How Can I Configure a PC to Do Bioinformatics Research?
1.8 What Information and Software Are Available?
1.9 Can I Learn a Programming Language Without Classes?
1.10 How Can I Use Web Information?
1.11 How Do I Understand Sequence Alignment Data?
1.12 How Do I Write a Program to Align Two Biological Sequences?
1.13 How Do I Predict Protein Structure from Sequence?
1.14 What Questions Can Bioinformatics Answer?
2. Computational Approaches to Biological Questions
2.1 Molecular Biology's Central Dogma
2.2 What Biologists Model
2.3 Why Biologists Model
2.4 Computational Methods Covered in This Book
2.5 A Computational Biology Experiment
II: The Bioinformatics Workstation
3. Setting Up Your Workstation
3.1 Working on a Unix System
3.2 Setting Up a Linux Workstation
3.3 How to Get Software Working
3.4 What Software Is Needed?
4. Files and Directories in Unix
4.1 Filesystem Basics
4.2 Commands for Working with Directories and Files
4.3 Working in a Multiuser Environment
5. Working on a Unix System
5.1 The Unix Shell
5.2 Issuing Commands on a Unix System
5.3 Viewing and Editing Files
5.4 Transformations and Filters
5.5 File Statistics and Comparisons
5.6 The Language of Regular Expressions
5.7 Unix Shell Scripts
5.8 Communicating with Other Computers
5.9 Playing Nicely with Others in a Shared Environment
III: Tools for Bioinformatics
6. Biological Research on the Web
6.1 Using Search Engines
6.2 Finding Scientific Articles
6.3 The Public Biological Databases
6.4 Searching Biological Databases
6.5 Depositing Data into the Public Databases
6.6 Finding Software
6.7 Judging the Quality of Information
7. Sequence Analysis, Pairwise Alignment, and Database Searching
7.1 Chemical Composition of Biomolecules
7.2 Composition of DNA and RNA
7.3 Watson and Crick Solve the Structure of DNA
7.4 Development of DNA Sequencing Methods
7.5 Genefinders and Feature Detection in DNA
7.6 DNA Translation
7.7 Pairwise Sequence Comparison
7.8 Sequence Queries Against Biological Databases
7.9 Multifunctional Tools for Sequence Analysis
8. Multiple Sequence Alignments, Trees, and Profiles
8.1 The Morphological to the Molecular
8.2 Multiple Sequence Alignment
8.3 Phylogenetic Analysis
8.4 Profiles and Motifs
9. Visualizing Protein Structures and Computing Structural Properties
9.1 A Word About Protein Structure Data
9.2 The Chemistry of Proteins
9.3 WebBased
Protein Structure Tools
9.4 Structure Visualization
9.5 Structure Classification
9.6 Structural Alignment
9.7 Structure Analysis
9.8 Solvent Accessibility and Interactions
9.9 Computing Physicochemical Properties
9.10 Structure Optimization
9.11 Protein Resource Databases
9.12 Putting It All Together
10. Predicting Protein Structure and Function from Sequence
10.1 Determining the Structures of Proteins
10.2 Predicting the Structures of Proteins
10.3 From 3D to 1D
10.4 Feature Detection in Protein Sequences
10.5 Secondary Structure Prediction
10.6 Predicting 3D Structure
10.7 Putting It All Together: A Protein Modeling Project
10.8 Summary
11. Tools for Genomics and Proteomics
11.1 From Sequencing Genes to Sequencing Genomes
11.2 Sequence Assembly
11.3 Accessing Genome Informationon the Web
11.4 Annotating and Analyzing Whole Genome Sequences
11.5 Functional Genomics: New Data Analysis Challenges
11.6 Proteomics
11.7 Biochemical Pathway Databases
11.8 Modeling Kinetics and Physiology
11.9 Summary
IV: Databases and Visualization
12. Automating Data Analysis with Perl
12.1 Why Perl?
12.2 Perl Basics
12.3 Pattern Matching and Regular Expressions
12.4 Parsing BLAST Output Using Perl
12.5 Applying Perl to Bioinformatics
13. Building Biological Databases
13.1 Types of Databases
13.2 Database Software
13.3 Introduction to SQL
13.4 Installing the MySQL DBMS
13.5 Database Design
13.6 Developing WebBased
Software That Interacts with Databases
14. Visualization and Data Mining
14.1 Preparing Your Data
14.2 Viewing Graphics
14.3 Sequence Data Visualization
14.4 Networks and Pathway Visualization
14.5 Working with Numerical Data
14.6 Visualization: Summary
14.7 Data Mining and Biological Information
