BioPerl



BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project. It is an open source software project which is still under active development. The first stable release was on June 11 2002, the most recent stable (in terms of API) release is 1.4.0 from December 2003. There are also unstable developer releases produced periodically, the most recent being 1.5.2 from December 62006. Version 1.5.2 is considered to be the most stable (in terms of bugs) version of BioPerl and believed to be suitable for most peoples requirements.

In order to take advantage of BioPerl, the user needs a basic understanding of the Perl programming language including an understanding of how to use Perl references, modules, objects and methods.

Benefits
BioPerl provides software modules for many of the typical tasks of bioinformatics programming. These include:


 * Accessing sequence data from local and remote databases
 * Transforming formats of database/ file records
 * Manipulating individual sequences
 * Searching for similar sequences
 * Creating and manipulating sequence alignments
 * Searching for genes and other structures on genomic DNA
 * Developing machine readable sequence annotations

Usage
In addition to being used directly by end-users, BioPerl has also provided the base for a wide variety of bioinformatic tools, including amongst others:


 * SynBrowse
 * GeneComber
 * TFBS
 * MIMOX
 * BioParser
 * Degenerate primer design
 * Querying the public databases
 * Current Comparative Table

New tools and algorithms from external developers are often integrated directly into BioPerl itself:


 * Dealing with phylogenetic trees and nested taxa
 * FPC Web tools