Chapter 12: Bioinformatics Programming Using Perl and Perl Modules

Perl (Practical Extraction and Report Language) is a high-level, yet relatively easy to use, programming language developed by Larry Wall. Since the release of version 1.0 in 1987, development has continued and expanded, with a large community of contributors who regularly add new functionality. Perl's file and text manipulation abilities make it well suited for tasks ranging from "quick" prototyping to complex and robust DNA and protein sequence analyses. Perl is a modular programming environment, comprising an exhaustive collection of contributed modules archived at the Comprehensive Perl Archive Network (CPAN). These modules facilitate tasks like database access, graphical programming, networking, and Web programming. Employing a combination of modules, one can quickly develop programs that minimize the drudgery and human intervention required with tasks associated with sequence analysis. The topics discussed in this chapter are not intended to be a definitive text on the subject matter, but rather an introduction to the advantages of using combinations of Open Source and community-evolved software and standards. Although this chapter exclusively deals with Perl and Perl modules, the reader is strongly encouraged to visit http://www.open-bio.org and examine the BioJava, BioPython, and BioRuby projects, which provide similar extensions to the traditional Java, Python, and Ruby languages. The goal in this chapter is to demonstrate the use of Perl and available modules for routinely performed bioinformatics tasks. Brief conceptual overviews and background information on related topics are also provded.