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
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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:
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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
Last Updated Saturday, April 13 2013 @ 04:17 PM EDT
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