Version

Bioperl version 1.6.1 is available in Louhi (front node only), Hippu, Vuori and Murska.

The perl version, which includes bioperl, is 5.8.9 in Hippu and Louhi. In Murska perl version 5.10.0 is used.

Description

Bioperl is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do. On the other hand, bioperl does provide reusable perl modules that facilitate writing perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.

Usage

 To use bioperl in Hippu or Murska, give command:

   module load bioperl

After this you can launch a bioperl program with command

perl my_bioperl_code.pm

#!/p/appl/bin/bioperl

./my_bioperl_code.pm

More information

More information about bioperl can be found form the homepage of bioperl.

• www.bioperl.org

• Bioperl course at CSC on May 2004 (includes video recordings)

Online bioperl course written at the Pasteur Institute can be found in address:

• http://www.pasteur.fr/recherche/unites/sis/formation/bioperl

The Bioperl installation includes documentation and examples too. In Hippu you can find these files in address:

   /v/linux26_x86_64/appl/molbio/bioperl/BioPerl-1.6.0/examples