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Mastering Perl for Bioinformatics
By James Tisdall
 
Publisher : O'Reilly
Pub Date : September 2003
ISBN : 0-596-00307-2
Pages : 396


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
  Index
  Reviews
  Reader Reviews
  Errata
Mastering Perl for Bioinformatics
By James Tisdall
 
Publisher : O'Reilly
Pub Date : September 2003
ISBN : 0-596-00307-2
Pages : 396


               
    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
      Section 1.1.  What Is a Module?
      Section 1.2.  Why Perl Modules?
      Section 1.3.  Namespaces
      Section 1.4.  Packages
      Section 1.5.  Defining Modules
      Section 1.6.  Storing Modules
      Section 1.7.  Writing Your First Perl Module
      Section 1.8.  Using Modules
      Section 1.9.  CPAN Modules
      Section 1.10.  Exercises
      Chapter 2.  Data Structures and String Algorithms
      Section 2.1.  Basic Perl Data Types
      Section 2.2.  References
      Section 2.3.  Matrices
      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
      Section 2.9.  Resources
      Section 2.10.  Exercises
      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
      Section 3.14.  Resources
      Section 3.15.  Exercises
      Chapter 4.  Sequence Formats and Inheritance
      Section 4.1.  Inheritance
      Section 4.2.  FileIO.pm: A Class to Read and Write Files
      Section 4.3.  SeqFileIO.pm: Sequence File Formats
      Section 4.4.  Resources
      Section 4.5.  Exercises
      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
      Section 5.5.  Resources
      Section 5.6.  Exercises
    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 6.10.  Resources
      Section 6.11.  Exercises
      Chapter 7.  Perl and the Web
      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 7.5.  Exercises
      Chapter 8.  Perl and Graphics
      Section 8.1.  Computer Graphics
      Section 8.2.  GD
      Section 8.3.  Adding GD Graphics to Restrictionmap.pm
      Section 8.4.  Making Graphs
      Section 8.5.  Resources
      Section 8.6.  Exercises
      Chapter 9.  Introduction to Bioperl
      Section 9.1.  The Growth of Bioperl
      Section 9.2.  Installing Bioperl
      Section 9.3.  Testing Bioperl
      Section 9.4.  Bioperl Problems
      Section 9.5.  Overview of Objects
      Section 9.6.  bptutorial.pl
      Section 9.7.  bptutorial.pl: sequence_manipulation Demo
      Section 9.8.  Using Bioperl Modules
    Part III:  Appendixes
      Appendix A.  Perl Summary
      Section A.1.  Command Interpretation
      Section A.2.  Comments
      Section A.3.  Scalar Values and Scalar Variables
      Section A.4.  Assignment
      Section A.5.  Statements and Blocks
      Section A.6.  Arrays
      Section A.7.  Hashes
      Section A.8.  Complex Data Structures
      Section A.9.  Operators
      Section A.10.  Operator Precedence
      Section A.11.  Basic Operators
      Section A.12.  Conditionals and Logical Operators
      Section A.13.  Binding Operators
      Section A.14.  Loops
      Section A.15.  Input/Output
      Section A.16.  Regular Expressions
      Section A.17.  Scalar and List Context
      Section A.18.  Subroutines
      Section A.19.  Modules and Packages
      Section A.20.  Object-Oriented Programming
      Section A.21.  Built-in Functions
      Appendix B.  Installing Perl
      Section B.1.  Installing Perl on Your Computer
      Section B.2.  Versions of Perl
      Section B.3.  Internet Access
      Section B.4.  Downloading
      Section B.5.  How to Run Perl Programs
      Section B.6.  Finding Help
    Colophon
    Index