BIOPERL: A Perl Extension for Bioinformatics

Abstract

Building a medium- to large-sized program usually requires you to divide tasks into several smaller, more manageable, and more interactive pieces. (A rule of thumb is that each "piece" should be about one or two printed pages in length, but this is just a general guideline.) An analogy can be made to building a microarray machine, which requires that you construct separate interacting pieces such as housing, temperature sensors and controls, robot arms to position the pipettes, hydraulic injection devices, and computer guidance for all these systems. Perl modules are essential to any Perl programmer. They are a great way to organize code into logical collections of interacting parts. They collect useful Perl subroutines and provide them to other programs (and programmers) in an organized and convenient fashion. The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics and life science research into a set of standard CPAN-style, well-documented, and freely available Perl modules. Perl provides unparalleled support for many tasks common in bioinformatics and life science research yet there are no standard Perl modules for biology. We hope to help fill this void.