Bioperl

Bioperl

BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Subversion modules in our repository.

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.

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