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Full Description
Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capacities in string handling, text processing, networking, and rapid prototyping, has emerged as the programming language of choice for biological data analysis. This text 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.
The range of topics covered in the book prepares the reader for enduring and emerging developments in critical areas of bioinformatics programming such as: gene finding; string alignment; methods of data storage and retrieval (SML and databases); modelling of networks (graphs and Petri nets); graphics (Tk); parallelization; interfacing with other programming languages; statistics (PDL); protein structure determination; and biological models of computation (DNA Computers). Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.
Contents
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 Exam ple 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 AUTOLO AD 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 Dat abases Popular Relational Databases Relati onal Database Definitions Structured Query Language Administering Your Database Relational D atabase Design Perl DBI and DBD Interface Modules A Rebase Database Implementation Additiona l 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.
