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.

Table of Contents

Foreword

Preface

Part I. Object-Oriented Programming in Perl

1. Modular Programming with Perl

     What Is a Module?

     Why Perl Modules?

     Namespaces

     Packages

     Defining Modules

     Storing Modules

     Writing Your First Perl Module

     Using Modules

     CPAN Modules

     Exercises

2. Data Structures and String Algorithms

     Basic Perl Data Types

     References

     Matrices

     Complex Data Structures

     Printing Complex Data Structures

     Data Structures in Action

     Dynamic Programming

     Approximate String Matching

     Resources

     Exercises

3. Object-Oriented Programming in Perl

     What Is Object-Oriented Programming?
     Using Perl Classes (Without Writing Them)

     Objects, Methods, and Classes in Perl

     Arrow Notation (->)

     Gene1: An Example of a Perl Class

     Details of the Gene1 Class

     Gene2.pm: A Second Example of a Perl Class
     Gene3.pm: A Third Example of a Perl Class

     How AUTOLOAD Works

     Cleaning Up Unused Objects with DESTROY

     Gene.pm: A Fourth Example of a Perl Class

     How to Document a Perl Class with POD

     Additional Topics

     Resources

     Exercises

4. Sequence Formats and Inheritance

     Inheritance

     FileIO.pm: A Class to Read and Write Files

     SeqFileIO.pm: Sequence File Formats

     Resources

     Exercises

5. A Class for Restriction Enzymes

     Envisioning an Object

     Rebase.pm: A Class Module

     Restriction.pm: Finding Recognition Sites

     Drawing Restriction Maps

     Resources

     Exercises

Part II. Perl and Bioinformatics

6. Perl and Relational Databases

     One Perl, Many Databases

     Popular Relational Databases

     Relational Database Definitions

     Structured Query Language

     Administering Your Database

     Relational Database Design

     Perl DBI and DBD Interface Modules

     A Rebase Database Implementation

     Additional Topics

     Resources

     Exercises

7. Perl and the Web

     How the Web Works

     Web Servers and Browsers

     The Common Gateway Interface

     Rebase: Building Dynamic Web Pages

     Exercises

8. Perl and Graphics

     Computer Graphics

     GD

     Adding GD Graphics to Restrictionmap.pm

     Making Graphs

     Resources

     Exercises

9. Introduction to Bioperl

     The Growth of Bioperl

     Installing Bioperl

     Testing Bioperl

     Bioperl Problems

     Overview of Objects

     bptutorial.pl

     bptutorial.pl: sequence_manipulation Demo

     Using Bioperl Modules

Part III. Appendixes

A. Perl Summary

B. Installing Perl

Index