Mastering Perl for Bioinformatics (Paperback)

James D. Tisdall



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



Part I. Object-Oriented Programming in Perl

1. Modular Programming with Perl

     What Is a Module?

     Why Perl Modules?



     Defining Modules

     Storing Modules

     Writing Your First Perl Module

     Using Modules

     CPAN Modules


2. Data Structures and String Algorithms

     Basic Perl Data Types



     Complex Data Structures

     Printing Complex Data Structures

     Data Structures in Action

     Dynamic Programming

     Approximate String Matching



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 A Second Example of a Perl Class A Third Example of a Perl Class

     How AUTOLOAD Works

     Cleaning Up Unused Objects with DESTROY A Fourth Example of a Perl Class

     How to Document a Perl Class with POD

     Additional Topics



4. Sequence Formats and Inheritance

     Inheritance A Class to Read and Write Files Sequence File Formats



5. A Class for Restriction Enzymes

     Envisioning an Object A Class Module Finding Recognition Sites

     Drawing Restriction Maps



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



7. Perl and the Web

     How the Web Works

     Web Servers and Browsers

     The Common Gateway Interface

     Rebase: Building Dynamic Web Pages


8. Perl and Graphics

     Computer Graphics


     Adding GD Graphics to

     Making Graphs



9. Introduction to Bioperl

     The Growth of Bioperl

     Installing Bioperl

     Testing Bioperl

     Bioperl Problems

     Overview of Objects sequence_manipulation Demo

     Using Bioperl Modules

Part III. Appendixes

A. Perl Summary

B. Installing Perl



《精通生物信息學的 Perl》涵蓋了核心 Perl 語言及其許多模塊擴展,並將它們置於生物數據和生物學界感興趣的問題的背景下進行介紹。這本書與《生物信息學的 Perl 入門》一起,構成了 Perl 編程的基礎課程。這第二卷完成了基礎 Perl 教程材料(引用、複雜數據結構、面向對象編程、使用模塊等,都以生物學的背景進行介紹),並介紹了一些在生物信息學中非常有興趣的高級主題。




《第一部分:Perl 中的面向對象編程》

《第 1 章:使用 Perl 進行模塊化編程》

《第 2 章:數據結構和字符串算法》

《第 3 章:Perl 中的面向對象編程》

《第 4 章:序列格式和繼承》

《第 5 章:限制酶的類》

《第二部分:Perl 和生物信息學》

《第 6 章:Perl 和關聯數據庫》

以上是《精通生物信息學的 Perl》的內容概要。本書將幫助讀者掌握 Perl 編程技巧,並將其應用於生物信息學領域中的問題。