Mastering Perl for Bioinformatics

Chapter 9. Introduction to Bioperl

Bioperl is a collection of more than 500 Perl modules for bioinformatics that have been written and maintained by an international group of volunteers. Bioperl is free (under a very unrestrictive copyright), and its home is http://bioperl.org.

One of the most difficult things about Bioperl is getting started using it. This is due to a scarcity of good documentation (which is being rectified) as well as the sheer size of the Bioperl module library. This chapter will help you get started using the Bioperl project software; it will guide you through the initial steps of getting the software, installing it, and exploring the tutorial and example material that it provides. After working through this chapter, you’ll be well prepared to delve deeper into the riches of Bioperl, and, if you’ve also worked through the object-oriented chapters earlier in this book, you’ll be in a good position to read the Bioperl code and contribute to the project yourself.

The modules in Bioperl are written in the object-oriented style. Perl programmers who do not know object-oriented programming can still use the Bioperl modules with just a bit of extra information, as outlined in Chapter 3.

The Bioperl modules cover various areas of bioinformatics, including some you’ve seen previously in this book. Although Bioperl includes some example programs, it is not meant to be a collection of complete user-ready programs. Rather, it’s implemented as a toolkit you can ...