• Index
• Reviews
• Errata
Mastering Perl for Bioinformatics
By Publisher: O''Reilly
Pub Date: September 2003
ISBN: 0-596-00307-2
Pages: 396
What You Need to Know to Use This Book
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 1.7. Writing Your First Perl Module
Chapter 2. Data Structures and String Algorithms
Section 2.1. Basic Perl Data Types
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
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
Chapter 4. Sequence Formats and Inheritance
Section 4.2. FileIO.pm: A Class to Read and Write Files
Section 4.3. SeqFileIO.pm: Sequence File Formats
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
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 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 8.1. Computer Graphics
Section 8.3. Adding GD Graphics to Restrictionmap.pm
Chapter 9. Introduction to Bioperl
Section 9.1. The Growth of Bioperl
Section 9.2. Installing Bioperl
Section 9.5. Overview of Objects
Section 9.7. bptutorial.pl: sequence_manipulation Demo
Section 9.8. Using Bioperl Modules
Section A.1. Command Interpretation
Section A.3. Scalar Values and Scalar Variables
Section A.5. Statements and Blocks
Section A.8. Complex Data Structures
Section A.10. Operator Precedence
Section A.12. Conditionals and Logical Operators
Section A.13. Binding Operators
Section A.16. Regular Expressions
Section A.17. Scalar and List Context
Section A.19. Modules and Packages
Section A.20. Object-Oriented Programming
Section A.21. Built-in Functions
Section B.1. Installing Perl on Your Computer
Section B.5. How to Run Perl Programs