1. Object-Oriented Programming in Perl

   1. Chapter 1 Modular Programming with Perl

      1. What Is a Module?
      2. Why Perl Modules?
      3. Namespaces
      4. Packages
      5. Defining Modules
      6. Storing Modules
      7. Writing Your First Perl Module
      8. Using Modules
      9. CPAN Modules
      10. Exercises

   2. Chapter 2 Data Structures and String Algorithms

      1. Basic Perl Data Types
      2. References
      3. Matrices
      4. Complex Data Structures
      5. Printing Complex Data Structures
      6. Data Structures in Action
      7. Dynamic Programming
      8. Approximate String Matching
      9. Resources
      10. Exercises

   3. Chapter 3 Object-Oriented Programming in Perl

      1. What Is Object-Oriented Programming?
      2. Using Perl Classes (Without Writing Them)
      3. Objects, Methods, and Classes in Perl
      4. Arrow Notation (->)
      5. Gene1: An Example of a Perl Class
      6. Details of the Gene1 Class
      7. Gene2.pm: A Second Example of a Perl Class
      8. Gene3.pm: A Third Example of a Perl Class
      9. How AUTOLOAD Works
      10. Cleaning Up Unused Objects with DESTROY
      11. Gene.pm: A Fourth Example of a Perl Class
      12. How to Document a Perl Class with POD
      13. Additional Topics
      14. Resources
      15. Exercises

   4. Chapter 4 Sequence Formats and Inheritance

      1. Inheritance
      2. FileIO.pm: A Class to Read and Write Files
      3. SeqFileIO.pm: Sequence File Formats
      4. Resources
      5. Exercises

   5. Chapter 5 A Class for Restriction Enzymes

      1. Envisioning an Object
      2. Rebase.pm: A Class Module
      3. Restriction.pm: Finding Recognition Sites
      4. Drawing Restriction Maps
      5. Resources
      6. Exercises

2. Perl and Bioinformatics

   1. Chapter 6 Perl and Relational Databases

      1. One Perl, Many Databases
      2. Popular Relational Databases
      3. Relational Database Definitions
      4. Structured Query Language
      5. Administering Your Database
      6. Relational Database Design
      7. Perl DBI and DBD Interface Modules
      8. A Rebase Database Implementation
      9. Additional Topics
      10. Resources
      11. Exercises

   2. Chapter 7 Perl and the Web

      1. How the Web Works
      2. Web Servers and Browsers
      3. The Common Gateway Interface
      4. Rebase: Building Dynamic Web Pages
      5. Exercises

   3. Chapter 8 Perl and Graphics

      1. Computer Graphics
      2. GD
      3. Adding GD Graphics to Restrictionmap.pm
      4. Making Graphs
      5. Resources
      6. Exercises

   4. Chapter 9 Introduction to Bioperl

      1. The Growth of Bioperl
      2. Installing Bioperl
      3. Testing Bioperl
      4. Bioperl Problems
      5. Overview of Objects
      6. bptutorial.pl
      7. bptutorial.pl: sequence_manipulation Demo
      8. Using Bioperl Modules

3. Appendixes

   1. Appendix A Perl Summary

      1. Command Interpretation
      2. Comments
      3. Scalar Values and Scalar Variables
      4. Assignment
      5. Statements and Blocks
      6. Arrays
      7. Hashes
      8. Complex Data Structures
      9. Operators
      10. Operator Precedence
      11. Basic Operators
      12. Conditionals and Logical Operators
      13. Binding Operators
      14. Loops
      15. Input/Output
      16. Regular Expressions
      17. Scalar and List Context
      18. Subroutines
      19. Modules and Packages
      20. Object-Oriented Programming
      21. Built-in Functions

   2. Appendix B Installing Perl

      1. Installing Perl on Your Computer
      2. Versions of Perl
      3. Internet Access
      4. Downloading
      5. How to Run Perl Programs
      6. Finding Help

1. 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 Mastering Perl for Bioinformatics is a North American bullfrog (Rana catesbeiana). It is native to the central and eastern United States, as well as southern portions of Canada. However, this bullfrog has since been introduced as far away from its native habitat as Asia, Europe, and Hawaii.

The North American bullfrog is the largest true frog in North America and can weigh over a pound. It can grow up to eight inches in length, although the norm is four to five inches. The gender of the bullfrog is ascertained by comparing the size of the external ear (the tympanum) relative to the size of the eye.

Bullfrogs are predators and also are cannibalistic. Their role in the environment is to control the population of insect pests as well as snakes and mice. In fact, the zeal of the North American bullfrog threatens to drive other frog species to extinction.

The generic name (rana) comes from the Latin for frog, while the species name (catesbeiana) honors an English naturalist. In the 18th century, Mark Catesby (1683--1749) produced the authoritative and exhaustive record of the flora and fauna found in the New World. Wealthy patrons in England eagerly received Catesby's regular shipments of specimens, including plants, birds, reptiles, insects, and frogs. Mary Anne Weeks Mayo was the production editor and copyeditor, and Marlowe Shaeffer was the proofreader, for Mastering Perl for Bioinformatics. Jane Ellin and Colleen Gorman provided quality control. Marlowe Shaeffer, Mary Agner, and James Quill provided production assistance. John Bickelhaupt wrote the index.

Ellie Volckhausen designed the cover of this book, based on a series design by Edie Freedman. The cover image is a 19th-century engraving from the Dover Pictorial Archive. Emma Colby produced the cover layout with QuarkXPress 4.1 using Adobe's ITC Garamond font.

David Futato designed the interior layout. This book was converted by Andrew Savikas to FrameMaker 5.5.6 with a format conversion tool created by Erik Ray, Jason McIntosh, Neil Walls, and Mike Sierra that uses Perl and XML technologies. 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 Reg Aubry.