Mastering Perl for Bioinformatics
Mastering Perl for Bioinformatics By James Tisdall
September 2003
Pages: 396

| Table of Contents | Index | Sample Chapter | Colophon

Table of Contents

  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

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