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