1. Chapter 1 Biology and Computer Science

   1. The Organization of DNA

   2. The Organization of Proteins

   3. In Silico

   4. Limits to Computation

2. Chapter 2 Getting Started with Perl

   1. A Low and Long Learning Curve

   2. Perl's Benefits

   3. Installing Perl on Your Computer

   4. How to Run Perl Programs

   5. Text Editors

   6. Finding Help

3. Chapter 3 The Art of Programming

   1. Individual Approaches to Programming

   2. Edit—Run—Revise (and Save)

   3. An Environment of Programs

   4. Programming Strategies

   5. The Programming Process

4. Chapter 4 Sequences and Strings

   1. Representing Sequence Data

   2. A Program to Store a DNA Sequence

   3. Concatenating DNA Fragments

   4. Transcription: DNA to RNA

   5. Using the Perl Documentation

   6. Calculating the Reverse Complement in Perl

   7. Proteins, Files, and Arrays

   8. Reading Proteins in Files

   9. Arrays

   10. Scalar and List Context

   11. Exercises

5. Chapter 5 Motifs and Loops

   1. Flow Control

   2. Code Layout

   3. Finding Motifs

   4. Counting Nucleotides

   5. Exploding Strings into Arrays

   6. Operating on Strings

   7. Writing to Files

   8. Exercises

6. Chapter 6 Subroutines and Bugs

   1. Subroutines

   2. Scoping and Subroutines

   3. Command-Line Arguments and Arrays

   4. Passing Data to Subroutines

   5. Modules and Libraries of Subroutines

   6. Fixing Bugs in Your Code

   7. Exercises

7. Chapter 7 Mutations and Randomization

   1. Random Number Generators

   2. A Program Using Randomization

   3. A Program to Simulate DNA Mutation

   4. Generating Random DNA

   5. Analyzing DNA

   6. Exercises

8. Chapter 8 The Genetic Code

   1. Hashes

   2. Data Structures and Algorithms for Biology

   3. The Genetic Code

   4. Translating DNA into Proteins

   5. Reading DNA from Files in FASTA Format

   6. Reading Frames

   7. Exercises

9. Chapter 9 Restriction Maps and Regular Expressions

   1. Regular Expressions

   2. Restriction Maps and Restriction Enzymes

   3. Perl Operations

   4. Exercises

10. Chapter 10 GenBank

    1. GenBank Files

    2. GenBank Libraries

    3. Separating Sequence and Annotation

    4. Parsing Annotations

    5. Indexing GenBank with DBM

    6. Exercises

11. Chapter 11 Protein Data Bank

    1. Overview of PDB

    2. Files and Folders

    3. PDB Files

    4. Parsing PDB Files

    5. Controlling Other Programs

    6. Exercises

12. Chapter 12 BLAST

    1. Obtaining BLAST

    2. String Matching and Homology

    3. BLAST Output Files

    4. Parsing BLAST Output

    5. Presenting Data

    6. Bioperl

    7. Exercises

13. Chapter 13 Further Topics

    1. The Art of Program Design

    2. Web Programming

    3. Algorithms and Sequence Alignment

    4. Object-Oriented Programming

    5. Perl Modules

    6. Complex Data Structures

    7. Relational Databases

    8. Microarrays and XML

    9. Graphics Programming

    10. Modeling Networks

    11. DNA Computers

1. Appendix A Resources

   1. Perl

   2. Computer Science

   3. Linux

   4. Bioinformatics

   5. Molecular Biology

2. Appendix B Perl Summary

   1. Command Interpretation

   2. Comments

   3. Scalar Values and Scalar Variables

   4. Assignment

   5. Statements and Blocks

   6. Arrays

   7. Hashes

   8. Operators

   9. Operator Precedence

   10. Basic Operators

   11. Conditionals and Logical Operators

   12. Binding Operators

   13. Loops

   14. Input/Output

   15. Regular Expressions

   16. Scalar and List Context

   17. Subroutines and Modules

   18. Built-in Functions

3. 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 animals on the cover of Beginning Perl for Bioinformatics are green frog (Rana clamitans) and American bullfrog (Rana catesbeiana) tadpoles.

Tadpoles are the larvae of frogs and toads. They are aquatic and when first hatched have large, round heads and long, flat tails. Through a complex process of metamorphosis, tadpoles change from small fishlike creatures to the more familiar frogs and toads. This process can take from 10 days to 3 years depending on the species.

During the first stages of metamorphosis, a tadpole's hind legs sprout, its head begins to flatten, and its tail becomes shorter. In its early life, a tadpole feeds primarily on diatoms, algae, and small quantities of zooplankton. As metamorphosis continues, it stops eating and begins to reabsorb its tail for sustenance while its digestive system changes from primarily vegetarian to carnivorous. During the final stages of metamorphosis, the tadpole's front legs appear, its jaws form, its skeleton hardens, and its gills disappear as the lungs develop. It soon begins to breathe air at the surface of the water. A short time later, the tadpole emerges from the water, reabsorbs the last of its tail, and hops off as a frog or a toad. Mary Anne Weeks Mayo was the production editor and copyeditor for Beginning Perl for Bioinformatics. Matt Hutchinson and Jane Ellin provided quality control. Edie Shapiro, Matt Hutchinson, and Derek DiMatteo provided production assistance. Ellen Troutman-Zaig 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. Emma Colby produced the cover layout with Quark XPress 4.1 using Adobe's ITC Garamond font.

Melanie Wang designed the interior layout, based on a series design by David Futato. Neil Walls converted the files from SGML to FrameMaker 5.5.6 using tools created by Mike Sierra. The text font is Linotype Birka; the heading font is Adobe Myriad Condensed; and the code font is LucasFont's TheSans Mono Condensed. The illustrations that appear in the book were produced by Robert Romano and Jessamyn Read using Macromedia FreeHand 9 and Adobe Photoshop 6. The tip and warning icons were drawn by Christopher Bing. This colophon was written by Lorrie LeJeune.