1. Introduction

   1. Chapter 1 Biology in the Computer Age

      1. How Is Computing Changing Biology?
      2. Isn't Bioinformatics Just About Building Databases?
      3. What Does Informatics Mean to Biologists?
      4. What Challenges Does Biology Offer Computer Scientists?
      5. What Skills Should a Bioinformatician Have?
      6. Why Should Biologists Use Computers?
      7. How Can I Configure a PC to Do Bioinformatics Research?
      8. What Information and Software Are Available?
      9. Can I Learn a Programming Language Without Classes?
      10. How Can I Use Web Information?
      11. How Do I Understand Sequence Alignment Data?
      12. How Do I Write a Program to Align Two Biological Sequences?
      13. How Do I Predict Protein Structure from Sequence?
      14. What Questions Can Bioinformatics Answer?

   2. Chapter 2 Computational Approaches to Biological Questions

      1. Molecular Biology's Central Dogma
      2. What Biologists Model
      3. Why Biologists Model
      4. Computational Methods Covered in This Book
      5. A Computational Biology Experiment

2. The Bioinformatics Workstation

   1. Chapter 3 Setting Up Your Workstation

      1. Working on a Unix System
      2. Setting Up a Linux Workstation
      3. How to Get Software Working
      4. What Software Is Needed?

   2. Chapter 4 Files and Directories in Unix

      1. Filesystem Basics
      2. Commands for Working with Directories and Files
      3. Working in a Multiuser Environment

   3. Chapter 5 Working on a Unix System

      1. The Unix Shell
      2. Issuing Commands on a Unix System
      3. Viewing and Editing Files
      4. Transformations and Filters
      5. File Statistics and Comparisons
      6. The Language of Regular Expressions
      7. Unix Shell Scripts
      8. Communicating with Other Computers
      9. Playing Nicely with Others in a Shared Environment

3. Tools for Bioinformatics

   1. Chapter 6 Biological Research on the Web

      1. Using Search Engines
      2. Finding Scientific Articles
      3. The Public Biological Databases
      4. Searching Biological Databases
      5. Depositing Data into the Public Databases
      6. Finding Software
      7. Judging the Quality of Information

   2. Chapter 7 Sequence Analysis, Pairwise Alignment, and Database Searching

      1. Chemical Composition of Biomolecules
      2. Composition of DNA and RNA
      3. Watson and Crick Solve the Structure of DNA
      4. Development of DNA Sequencing Methods
      5. Genefinders and Feature Detection in DNA
      6. DNA Translation
      7. Pairwise Sequence Comparison
      8. Sequence Queries Against Biological Databases
      9. Multifunctional Tools for Sequence Analysis

   3. Chapter 8 Multiple Sequence Alignments, Trees, and Profiles

      1. The Morphological to the Molecular
      2. Multiple Sequence Alignment
      3. Phylogenetic Analysis
      4. Profiles and Motifs

   4. Chapter 9 Visualizing Protein Structures and Computing Structural Properties

      1. A Word About Protein Structure Data
      2. The Chemistry of Proteins
      3. Web-Based Protein Structure Tools
      4. Structure Visualization
      5. Structure Classification
      6. Structural Alignment
      7. Structure Analysis
      8. Solvent Accessibility and Interactions
      9. Computing Physicochemical Properties
      10. Structure Optimization
      11. Protein Resource Databases
      12. Putting It All Together

   5. Chapter 10 Predicting Protein Structure and Function from Sequence

      1. Determining the Structures of Proteins
      2. Predicting the Structures of Proteins
      3. From 3D to 1D
      4. Feature Detection in Protein Sequences
      5. Secondary Structure Prediction
      6. Predicting 3D Structure
      7. Putting It All Together: A Protein Modeling Project
      8. Summary

   6. Chapter 11 Tools for Genomics and Proteomics

      1. From Sequencing Genes to Sequencing Genomes
      2. Sequence Assembly
      3. Accessing Genome Informationon the Web
      4. Annotating and Analyzing Whole Genome Sequences
      5. Functional Genomics: New Data Analysis Challenges
      6. Proteomics
      7. Biochemical Pathway Databases
      8. Modeling Kinetics and Physiology
      9. Summary

4. Databases and Visualization

   1. Chapter 12 Automating Data Analysis with Perl

      1. Why Perl?
      2. Perl Basics
      3. Pattern Matching and Regular Expressions
      4. Parsing BLAST Output Using Perl
      5. Applying Perl to Bioinformatics

   2. Chapter 13 Building Biological Databases

      1. Types of Databases
      2. Database Software
      3. Introduction to SQL
      4. Installing the MySQL DBMS
      5. Database Design
      6. Developing Web-Based Software That Interacts with Databases

   3. Chapter 14 Visualization and Data Mining

      1. Preparing Your Data
      2. Viewing Graphics
      3. Sequence Data Visualization
      4. Networks and Pathway Visualization
      5. Working with Numerical Data
      6. Visualization: Summary
      7. Data Mining and Biological Information

1. Bibliography

2. Colophon

Our look is the result of reader comments, our own experimentation, and feedback from distribution channels. Distinctive covers complement our distinctive approach to technical topics, breathing personality and life into potentially dry subjects. The animal on the cover of Developing Bioinformatics Computer Skills is Caenorhabditis elegans, a small nematode worm. Unlike many of its nastier parasitic cousins, C. elegans lives in the soil where it feeds on microbes and bacteria. It grows to about 1 mm in length.

In spite of its status as a "primitive" organism, C. elegans shares with H. sapiens many essential biological characteristics. C. elegans begins life as a single cell that divides and grows to form a multicellular adult. It has a nervous system and a brain (more properly known as the circumpharyngeal ring) and a muscular system that supports locomotion. It exhibits behavior and is capable of rudimentary learning. Like humans, it comes in two sexes, but in C. elegans those sexes consist of a male and a self-fertilizing hermaphrodite. C. elegans is easily grown in large numbers in the laboratory, has a short (2-3 week) lifespan, and can be manipulated in sophisticated experiments. These characteristics make it an ideal organism for scientific research.

The C. elegans hermaphrodite has 959 cells, 300 of which are neurons, and 81 of which are muscle cells. The entire cell lineage has been traced through development. The adult has a number of sensory organs in the head region which respond to taste, smell, touch, and temperature. Although it has no eyes, it does react slightly to light. C. elegans has approximately 17,800 distinct genes, and its genome has been completely sequenced. Along with the fruit fly, the mouse, and the weed Arabidopsis, C. elegans has become one of the most studied model organisms in biology since Sydney Brenner first focused his attention on it decades ago. Mary Anne Weeks Mayo was the production editor and copyeditor for Developing Bioinformatics Computer Skills. Rachel Wheeler proofread the book. Linley Dolby and Sheryl Avruch provided quality control. Gabe Weiss, Edie Shapiro, Matt Hutchinson, and Sada Preisch provided production assistance. Joe Wizda wrote the index.

Ellie Volckhausen designed the cover of this book, based on a series design by Edie Freedman. The cover image is an original illustration created by Lorrie LeJeune, based on a photograph supplied by Leon Avery at the University of Texas Southwestern Medical Center. Emma Colby produced the cover layout with QuarkXPress 4.1 using Adobe's ITC Garamond font.

Melanie Wang designed the interior layout based on a series design by Nancy Priest. Cliff Dyer converted the files from MSWord to FrameMaker 5.5 using tools created by Mike Sierra. The text and heading fonts are ITC Garamond Light and Garamond Book; the code font is Constant Willison. The illustrations for this book were created by Robert Romano and Lucy Muellner using Macromedia Freehand 9 and Adobe Photoshop 6. This colophon was written by Lorrie LeJeune.

Whenever possible, our books use a durable and flexible lay-flat binding. If the page count exceeds this binding's limit, perfect binding is used.