BioPerl

BioPerl
Initial release 11 June 2002 (2002-06-11)
Stable release 1.6.9 / 14 April 2011; 9 months ago (2011-04-14)
Preview release nightly builds
Development status Active
Written in Perl
Platform Cross-platform
Type Bioinformatics
License Artistic License and GPL
Website bioperl.org

BioPerl [1] is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project.[2]

It is an active open source software project supported by the Open Bioinformatics Foundation.

Its history can be traced to a September 1996 mailing list discussion. The first stable release was on 11 June 2002; the most recent stable (in terms of API) release is 1.6.1 from October 2009. There are also developer releases produced periodically. Version 1.6.0 is considered to be the most stable (in terms of bugs) version of BioPerl and is recommended for everyday use, but the nightly builds are also extremely stable, and many BioPerl users stay current with those.

In order to take advantage of BioPerl, the user needs a basic understanding of the Perl programming language including an understanding of how to use Perl references, modules, objects and methods.

Contents

Features

BioPerl provides software modules for many of the typical tasks of bioinformatics programming. These include:

Usage

In addition to being used directly by end-users, [3] BioPerl has also provided the base for a wide variety of bioinformatic tools, including amongst others:

New tools and algorithms from external developers are often integrated directly into BioPerl itself:

Related Programming Languages

Several related bioinformatics programming languages exist, including:

See also

References

For a complete, up-to-date list of BioPerl references, please see BioPerl publications

  1. ^ Stajich J, Block D, Boulez K, Brenner S, Chervitz S, Dagdigian C, Fuellen G, Gilbert J, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall C, Osborne B, Pocock M, Schattner P, Senger M, Stein L, Stupka E, Wilkinson M, Birney E (2002). "The Bioperl Toolkit: Perl Modules for the Life Sciences". Genome Res 12 (10): 1611–8. doi:10.1101/gr.361602. PMC 187536. PMID 12368254. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=187536. 
  2. ^ Lincoln Stein (1996). "How Perl saved the human genome project". The Perl Journal 1 (2). http://www.bioperl.org/wiki/How_Perl_saved_human_genome. Retrieved 2009-02-25 (Bioperl.org). 
  3. ^ Khaja R, MacDonald J, Zhang J, Scherer S (2006). "Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes". Methods Mol Biol 338: 9–20. doi:10.1385/1-59745-097-9:9. ISBN 1-59745-097-9. PMID 16888347. 
  4. ^ Pan X, Stein L, Brendel V (2005). "SynBrowse: a synteny browser for comparative sequence analysis". Bioinformatics 21 (17): 3461–8. doi:10.1093/bioinformatics/bti555. PMID 15994196. 
  5. ^ Shah S, McVicker G, Mackworth A, Rogic S, Ouellette B (2003). "GeneComber: combining outputs of gene prediction programs for improved results". Bioinformatics 19 (10): 1296–7. doi:10.1093/bioinformatics/btg139. PMID 12835277. 
  6. ^ Lenhard B, Wasserman W (2002). "TFBS: Computational framework for transcription factor binding site analysis". Bioinformatics 18 (8): 1135–6. doi:10.1093/bioinformatics/18.8.1135. PMID 12176838. 
  7. ^ Huang J, Gutteridge A, Honda W, Kanehisa M (2006). "MIMOX: a web tool for phage display based epitope mapping". BMC Bioinformatics 7: 451. doi:10.1186/1471-2105-7-451. PMC 1618411. PMID 17038191. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1618411. 
  8. ^ Catanho M, Mascarenhas D, Degrave W, de Miranda A (2006). "BioParser: a tool for processing of sequence similarity analysis reports". Appl Bioinformatics 5 (1): 49–53. doi:10.2165/00822942-200605010-00007. PMID 16539538. 
  9. ^ Wei X, Kuhn D, Narasimhan G (2003). "Degenerate primer design via clustering". Proc IEEE Comput Soc Bioinform Conf 2: 75–83. PMID 16452781. 
  10. ^ Croce O, Lamarre M, Christen R (2006). "Querying the public databases for sequences using complex keywords contained in the feature lines". BMC Bioinformatics 7: 45. doi:10.1186/1471-2105-7-45. PMC 1403806. PMID 16441875. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1403806. 
  11. ^ Landsteiner B, Olson M, Rutherford R (2005). "Current Comparative Table (CCT) automates customized searches of dynamic biological databases". Nucleic Acids Res 33 (Web Server issue): W770–3. doi:10.1093/nar/gki432. PMC 1160193. PMID 15980582. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1160193. 
  12. ^ Llabrés M, Rocha J, Rosselló F, Valiente G (2006). "On the ancestral compatibility of two phylogenetic trees with nested taxa". J Math Biol 53 (3): 340–64. doi:10.1007/s00285-006-0011-4. PMID 16823581. 
  13. ^ Pampanwar V, Engler F, Hatfield J, Blundy S, Gupta G, Soderlund C (2005). "FPC Web Tools for Rice, Maize, and Distribution". Plant Physiol 138 (1): 116–26. doi:10.1104/pp.104.056291. PMC 1104167. PMID 15888684. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1104167. 

External links