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BioPerl

BioPerl

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 laboraties, and pharmaceutical companies of all sizes.

 BioPerl 1.6.9

Price
Free to download

Size
6.6MB
License

GNU GPL and Perl Artistic License

Developer
Sendu Bala, Chris Dagdigian, Christopher Fields, Mark Jensen, Hilmar Lapp, Heikki Lehväslaiho, Aaron Mackey, Brian Osborne, Jason Stajic, Lincoln Stein, and many others

Website
www.bioperl.org

System Requirements
Perl 5.6.1 or higher
CPAN and a number of perl modules
GBrowse

Support Sites:
Documentation, HOWTOs, FAQ, Tutorial, Mailing Lists

Selected Reviews:

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

Return to Bioinformatics Tools Home Page

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Last Updated Saturday, September 07 2013 @ 04:47 AM EDT


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