Mastering Perl for Bioinformatics (Paperback)

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Mastering Perl for Bioinformatics (Paperback)

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內容描述

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
Foreword
Preface
Part I. Object-Oriented Programming in Perl

1. Modular Programming with Perl      What Is a
   Module?      Why Perl Modules?    
    Namespaces      Packages    
    Defining Modules      Storing Modules
        Writing Your First Perl Module    
    Using Modules      CPAN Modules  
      Exercises
2. Data Structures and String Algorithms    
    Basic Perl Data Types      References
        Matrices      Complex Data
   Structures      Printing Complex Data Structures
        Data Structures in Action    
    Dynamic Programming      Approximate String
   Matching      Resources    
    Exercises

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      Gene2.pm: A Second
   Example of a Perl Class      Gene3.pm: A Third Example of a
   Perl Class      How AUTOLOAD Works  
      Cleaning Up Unused Objects with DESTROY    
    Gene.pm: A Fourth Example of a Perl Class      How
   to Document a Perl Class with POD      Additional Topics
        Resources      Exercises

4. Sequence Formats and Inheritance    
    Inheritance      FileIO.pm: A Class to Read and
   Write Files      SeqFileIO.pm: Sequence File Formats
        Resources      Exercises

5. A Class for Restriction Enzymes    
    Envisioning an Object      Rebase.pm: A Class
   Module      Restriction.pm: Finding Recognition Sites
        Drawing Restriction Maps    
    Resources      Exercises
   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      Resources
        Exercises
7. Perl and the Web      How the Web Works
        Web Servers and Browsers    
    The Common Gateway Interface      Rebase: Building
   Dynamic Web Pages      Exercises
8. Perl and Graphics      Computer Graphics
        GD      Adding GD Graphics
   to Restrictionmap.pm      Making Graphs  
      Resources      Exercises
9. Introduction to Bioperl      The Growth of
   Bioperl      Installing Bioperl    
    Testing Bioperl      Bioperl Problems
        Overview of Objects    
    bptutorial.pl      bptutorial.pl:
   sequence_manipulation Demo      Using Bioperl Modules

Part III. Appendixes
A. Perl Summary
B. Installing Perl
Index