Mastering Perl for Bioinformatics

James Tisdall has worked as a musician, a programmer at Bell Labs (where he programmed for speech research and discovered a formal language for musical rhythm), and as a bioinformaticist at Mercator Genetics in Menlo Park, California, and at Fox Chase Cancer Center in Philadelphia. He has a B.A. in mathematics from the City College of New York and an M.S. in computer science from Columbia University; he is working towards a Ph.D. in computer science at the University of Pennsylvania. In his spare time, Jim teaches computer music at the Settlement Music School in Philadelphia. He is also the author of O'Reilly's Beginning Perl for Bioinformatics.

• 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.