---

Mastering Perl for Bioinformatics

ISBN: 0596003072
EAN: 2147483647

Year: 2003
Pages: 156

Authors: James D. Tisdall

BUY ON AMAZON

• Main Page
• Table of content
• Copyright
• 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 InputOutput
• 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
• Colophon
• Index
• Index SYMBOL
• Index A
• Index B
• Index C
• Index D
• Index E
• Index F
• Index G
• Index H
• Index I
• Index J
• Index K
• Index L
• Index M
• Index N
• Index O
• Index P
• Index Q
• Index R
• Index S
• Index T
• Index U
• Index V
• Index W