Cognia DocBook

Beginners HOWTO

Brian Osborne

Cognia Corporation


 
        

James Thompson



 
        

This document is copyright Brian Osborne, 2004. For reproduction other than personal use please contact brian at cognia.com.

2005-02-08

Abstract

This is a HOWTO written in DocBook (XML) that talks about using Bioperl, for biologists who would like to learn more about writing their own bioinformatics scripts using Bioperl.

What is Bioperl? It is an open source bioinformatics toolkit used by researchers all over the world. If you're looking for a script built to fit your exact need it's likely you won't find it in Bioperl. What you will find is a diverse set of Perl modules that will enable you to write your own script, and a commmunity of people who are willing to help you.

Table of Contents

1. Introduction
2. Installing Bioperl
3. Getting Assistance
4. Perl Itself
5. Starting to write a script on Unix
6. Creating a sequence, and an object
7. Writing a sequence to a file
8. Retrieving a sequence from a file
9. Retrieving a sequence from a database
10. The Sequence object
11. Example Sequence objects
12. BLAST
13. Indexing for Fast Retrieval
14. More on Bioperl
15. Perl's Documentation System
16. The Basics of Perl Objects
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