Preparing your results

Our searching services are busy right now. Your search will reload in five seconds.

X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

The Bioperl toolkit: Perl modules for the life sciences.

Genome research | Oct 7, 2002

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.

Pubmed ID: 12368254 RIS Download

Mesh terms: Algorithms | Animals | Biological Science Disciplines | Computational Biology | Computer Graphics | Database Management Systems | Databases, Genetic | Humans | Internet | Online Systems | Software | Software Design | Systems Integration

Research resources used in this publication

None found

Research tools detected in this publication

None found

Data used in this publication

None found

Associated grants

  • Agency: NIGMS NIH HHS, Id: T32 GM007754
  • Agency: NHGRI NIH HHS, Id: U41 HG000739
  • Agency: NHGRI NIH HHS, Id: 1 K32 HG00056
  • Agency: NHGRI NIH HHS, Id: P41 HG002223
  • Agency: NHGRI NIH HHS, Id: K22 HG000064
  • Agency: NHGRI NIH HHS, Id: K22 HG000056
  • Agency: NHGRI NIH HHS, Id: K22 HG-00064-01
  • Agency: NHGRI NIH HHS, Id: P41 HG000739
  • Agency: NHGRI NIH HHS, Id: P41HG02223
  • Agency: NHGRI NIH HHS, Id: HG00739
  • Agency: NIGMS NIH HHS, Id: T32 GM07754-22

Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.