Mastering Perl for Bioinformatics (Paperback)

James D. Tisdall



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



Part I. Object-Oriented Programming in Perl

1. Modular Programming with Perl

     What Is a Module?

     Why Perl Modules?



     Defining Modules

     Storing Modules

     Writing Your First Perl Module

     Using Modules

     CPAN Modules


2. Data Structures and String Algorithms

     Basic Perl Data Types



     Complex Data Structures

     Printing Complex Data Structures

     Data Structures in Action

     Dynamic Programming

     Approximate String Matching



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 A Second Example of a Perl Class A Third Example of a Perl Class

     How AUTOLOAD Works

     Cleaning Up Unused Objects with DESTROY A Fourth Example of a Perl Class

     How to Document a Perl Class with POD

     Additional Topics



4. Sequence Formats and Inheritance

     Inheritance A Class to Read and Write Files Sequence File Formats



5. A Class for Restriction Enzymes

     Envisioning an Object A Class Module Finding Recognition Sites

     Drawing Restriction Maps



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



7. Perl and the Web

     How the Web Works

     Web Servers and Browsers

     The Common Gateway Interface

     Rebase: Building Dynamic Web Pages


8. Perl and Graphics

     Computer Graphics


     Adding GD Graphics to

     Making Graphs



9. Introduction to Bioperl

     The Growth of Bioperl

     Installing Bioperl

     Testing Bioperl

     Bioperl Problems

     Overview of Objects sequence_manipulation Demo

     Using Bioperl Modules

Part III. Appendixes

A. Perl Summary

B. Installing Perl