BioPerl is a collection of Perl tools for computational molecular biology.
The BioPerl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g. Ensembl.
BioPerl 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 Git modules.
BioPerl is used by many large and small academic laboratories, and pharmaceutical companies of all sizes.
Features include:
- Accessing nucleotide and peptide 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.
- Provides the base for many different bioinformatic tools including: SynBrowse, TFBS, MIMOX, BioParser, GeneComber, and many others.
Website: bioperl.org
Support: GitHub Code Repository
Developer: Sendu Bala, Chris Dagdigian, Christopher Fields, Mark Jensen, Hilmar Lapp, Heikki Lehväslaiho, Aaron Mackey, Brian Osborne, Jason Stajic, Lincoln Stein, and many others
License: GNU General Public License and Perl Artistic License
BioPerl is written in Perl. Learn Perl with our recommended free books and free tutorials.
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