Table of Contents
Chapter 1 Biology in the Computer Age
- How Is Computing Changing Biology?
- Isn’t Bioinformatics Just About Building Databases?
- What Does Informatics Mean to Biologists?
- What Challenges Does Biology Offer Computer Scientists?
- What Skills Should a Bioinformatician Have?
- Why Should Biologists Use Computers?
- How Can I Configure a PC to Do Bioinformatics Research?
- What Information and Software Are Available?
- Can I Learn a Programming Language Without Classes?
- How Can I Use Web Information?
- How Do I Understand Sequence Alignment Data?
- How Do I Write a Program to Align Two Biological Sequences?
- How Do I Predict Protein Structure from Sequence?
- What Questions Can Bioinformatics Answer?
Chapter 2 Computational Approaches to Biological Questions
- Molecular Biology’s Central Dogma
- What Biologists Model
- Why Biologists Model
- Computational Methods Covered in This Book
- A Computational Biology Experiment
The Bioinformatics Workstation
Chapter 3 Setting Up Your Workstation
- Working on a Unix System
- Setting Up a Linux Workstation
- How to Get Software Working
- What Software Is Needed?
Chapter 4 Files and Directories in Unix
- Filesystem Basics
- Commands for Working with Directories and Files
- Working in a Multiuser Environment
Chapter 5 Working on a Unix System
- The Unix Shell
- Issuing Commands on a Unix System
- Viewing and Editing Files
- Transformations and Filters
- File Statistics and Comparisons
- The Language of Regular Expressions
- Unix Shell Scripts
- Communicating with Other Computers
- Playing Nicely with Others in a Shared Environment
Tools for Bioinformatics
Chapter 6 Biological Research on the Web
- Using Search Engines
- Finding Scientific Articles
- The Public Biological Databases
- Searching Biological Databases
- Depositing Data into the Public Databases
- Finding Software
- Judging the Quality of Information
Chapter 7 Sequence Analysis, Pairwise Alignment, and Database Searching
- Chemical Composition of Biomolecules
- Composition of DNA and RNA
- Watson and Crick Solve the Structure of DNA
- Development of DNA Sequencing Methods
- Genefinders and Feature Detection in DNA
- DNA Translation
- Pairwise Sequence Comparison
- Sequence Queries Against Biological Databases
- Multifunctional Tools for Sequence Analysis
Chapter 8 Multiple Sequence Alignments, Trees, and Profiles
- The Morphological to the Molecular
- Multiple Sequence Alignment
- Phylogenetic Analysis
- Profiles and Motifs
Chapter 9 Visualizing Protein Structures and Computing Structural Properties
- A Word About Protein Structure Data
- The Chemistry of Proteins
- Web-Based Protein Structure Tools
- Structure Visualization
- Structure Classification
- Structural Alignment
- Structure Analysis
- Solvent Accessibility and Interactions
- Computing Physicochemical Properties
- Structure Optimization
- Protein Resource Databases
- Putting It All Together
Chapter 10 Predicting Protein Structure and Function from Sequence
- Determining the Structures of Proteins
- Predicting the Structures of Proteins
- From 3D to 1D
- Feature Detection in Protein Sequences
- Secondary Structure Prediction
- Predicting 3D Structure
- Putting It All Together: A Protein Modeling Project
Chapter 11 Tools for Genomics and Proteomics
- From Sequencing Genes to Sequencing Genomes
- Sequence Assembly
- Accessing Genome Informationon the Web
- Annotating and Analyzing Whole Genome Sequences
- Functional Genomics: New Data Analysis Challenges
- Biochemical Pathway Databases
- Modeling Kinetics and Physiology
Databases and Visualization
Chapter 12 Automating Data Analysis with Perl
- Why Perl?
- Perl Basics
- Pattern Matching and Regular Expressions
- Parsing BLAST Output Using Perl
- Applying Perl to Bioinformatics
Chapter 13 Building Biological Databases
- Types of Databases
- Database Software
- Introduction to SQL
- Installing the MySQL DBMS
- Database Design
- Developing Web-Based Software That Interacts with Databases
Chapter 14 Visualization and Data Mining
- Preparing Your Data
- Viewing Graphics
- Sequence Data Visualization
- Networks and Pathway Visualization
- Working with Numerical Data
- Visualization: Summary
- Data Mining and Biological Information