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Mastering Perl for Bioinformatics covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with Beginning Perl for Bioinformatics, forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules–all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics. Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author’s well-balanced approach to applying Perl’s analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.

Copyright
Foreword
Preface
About This Book
What You Need to Know to Use This Book
Organization of This Book
Conventions Used in This Book
Comments and Questions
Acknowledgments
Part I: Object-Oriented Programming in Perl
Chapter 1. Modular Programming with Perl
Section 1.1. What Is a Module?
Section 1.2. Why Perl Modules?
Section 1.3. Namespaces
Section 1.4. Packages
Section 1.5. Defining Modules
Section 1.6. Storing Modules
Section 1.7. Writing Your First Perl Module
Section 1.8. Using Modules
Section 1.9. CPAN Modules
Section 1.10. Exercises
Chapter 2. Data Structures and String Algorithms
Section 2.1. Basic Perl Data Types
Section 2.2. References
Section 2.3. Matrices
Section 2.4. Complex Data Structures
Section 2.5. Printing Complex Data Structures
Section 2.6. Data Structures in Action
Section 2.7. Dynamic Programming
Section 2.8. Approximate String Matching
Section 2.9. Resources
Section 2.10. Exercises
Chapter 3. Object-Oriented Programming in Perl
Section 3.1. What Is Object-Oriented Programming?
Section 3.2. Using Perl Classes (Without Writing Them)
Section 3.3. Objects, Methods, and Classes in Perl
Section 3.4. Arrow Notation (->)
Section 3.5. Gene1: An Example of a Perl Class
Section 3.6. Details of the Gene1 Class
Section 3.7. Gene2.pm: A Second Example of a Perl Class
Section 3.8. Gene3.pm: A Third Example of a Perl Class
Section 3.9. How AUTOLOAD Works
Section 3.10. Cleaning Up Unused Objects with DESTROY
Section 3.11. Gene.pm: A Fourth Example of a Perl Class
Section 3.12. How to Document a Perl Class with POD
Section 3.13. Additional Topics
Section 3.14. Resources
Section 3.15. Exercises
Chapter 4. Sequence Formats and Inheritance
Section 4.1. Inheritance
Section 4.2. FileIO.pm: A Class to Read and Write Files
Section 4.3. SeqFileIO.pm: Sequence File Formats
Section 4.4. Resources
Section 4.5. Exercises
Chapter 5. A Class for Restriction Enzymes
Section 5.1. Envisioning an Object
Section 5.2. Rebase.pm: A Class Module
Section 5.3. Restriction.pm: Finding Recognition Sites
Section 5.4. Drawing Restriction Maps
Section 5.5. Resources
Section 5.6. Exercises
Part II: Perl and Bioinformatics
Chapter 6. Perl and Relational Databases
Section 6.1. One Perl, Many Databases
Section 6.2. Popular Relational Databases
Section 6.3. Relational Database Definitions
Section 6.4. Structured Query Language
Section 6.5. Administering Your Database
Section 6.6. Relational Database Design
Section 6.7. Perl DBI and DBD Interface Modules
Section 6.8. A Rebase Database Implementation
Section 6.9. Additional Topics
Section 6.10. Resources
Section 6.11. Exercises
Chapter 7. Perl and the Web
Section 7.1. How the Web Works
Section 7.2. Web Servers and Browsers
Section 7.3. The Common Gateway Interface
Section 7.4. Rebase: Building Dynamic Web Pages
Section 7.5. Exercises
Chapter 8. Perl and Graphics
Section 8.1. Computer Graphics
Section 8.2. GD
Section 8.3. Adding GD Graphics to Restrictionmap.pm
Section 8.4. Making Graphs
Section 8.5. Resources
Section 8.6. Exercises
Chapter 9. Introduction to Bioperl
Section 9.1. The Growth of Bioperl
Section 9.2. Installing Bioperl
Section 9.3. Testing Bioperl
Section 9.4. Bioperl Problems
Section 9.5. Overview of Objects
Section 9.6. bptutorial.pl
Section 9.7. bptutorial.pl: sequence_manipulation Demo
Section 9.8. Using Bioperl Modules
Part III: Appendixes
Appendix A. Perl Summary
Section A.1. Command Interpretation
Section A.2. Comments
Section A.3. Scalar Values and Scalar Variables
Section A.4. Assignment
Section A.5. Statements and Blocks
Section A.6. Arrays
Section A.7. Hashes
Section A.8. Complex Data Structures
Section A.9. Operators
Section A.10. Operator Precedence
Section A.11. Basic Operators
Section A.12. Conditionals and Logical Operators
Section A.13. Binding Operators
Section A.14. Loops
Section A.15. Input/Output
Section A.16. Regular Expressions
Section A.17. Scalar and List Context
Section A.18. Subroutines
Section A.19. Modules and Packages
Section A.20. Object-Oriented Programming
Section A.21. Built-in Functions
Appendix B. Installing Perl
Section B.1. Installing Perl on Your Computer
Section B.2. Versions of Perl
Section B.3. Internet Access
Section B.4. Downloading
Section B.5. How to Run Perl Programs
Section B.6. Finding Help
Colophon
Index
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