Introduction to BioPerl h Kumar National Resource Centre/Free and Open Source Software Chennai What is BioPerl? a set of Perl modules for. and It will cover both learning Perl and bioperl. have an advice for you If you are totally beginner and you just want to learn any programming. To that end, Bioperl provides extensive documentation of all of the routines in each module, a graphical diagram of the objects in the toolkit, and a set of tutorials.

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Bioperl is a collection of more than Perl modules for bioinformatics that have been written and maintained by an international group of volunteers. Bioperl is free under a very unrestrictive copyrightand its home is http: 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.

BioPerl: BioperlOverview

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 dip into for help when writing your own programs.

Its goal is to provide good working solutions to common bioinformatics tasks and to speed your program development. One of the best things about Bioperl is that it’s an biopel source project, meaning that interested developers are invited to contribute by writing code or in other ways, and the code is available to anyone interested.

If you’ve learned enough about Perl for bioinformatics to have worked through a good portion of this book, you’ll find plenty of opportunity biooerl get involved in Bioperl if you have the time and inclination.


Home Programming Perl for bioinformatics. Organization of This Book. Conventions Used in This Book.

BioPerl Tutorial: Extracting DNA Sequences From a Database

Object-Oriented Programming in Perl. Modular Programming with Perl. Data Structures and String Algorithms. An Example of a Perl Class. A Second Example of a Perl Class. A Third Example of a Perl Class.

Beginning Perl for Bioinformatics by James Tisdall

A Fourth Example of a Perl Class. Sequence Formats and Inheritance.

A Class to Read and Write Files. A Class for Restriction Enzymes. Perl and Relational Databases. Perl and the Web. Building Dynamic Web Pages.