BioPerl

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BioPerl
Initial release 11 June 2002 (2002-06-11)
Stable release 1.6.923 / 19 December 2013 (2013-12-19)
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][2] 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.[3]

Background

BioPerl is an active open source software project supported by the Open Bioinformatics Foundation. The first set of Perl codes of Bioperl was created by Tim Hubbard and Jong Bhak at MRC Centre Cambridge where the first genome sequencing was carried out by Fred Sanger. MRC Centre was one of the hubs and birth places of modern bioinformatics as it had large amount of DNA sequences and 3D protein structures. The name Bioperl was coined jointly by Jong Bhak and Steve Brenner in a small room of Centre for Protein Engineering (CPE) of MRC Centre where Alan Fersht was the director. In that small room, Cyrus Chothia and Tim Hubbard were working with some of their Ph.D. students and colleagues. Tim Hubbard is an expert Perl programmer and he was using th_lib.pl that contained many useful Perl subroutines for bioinformatics. Jong Bhak, being the first Ph.D. student of Tim Hubbard created jong_lib.pl. Jong merged the two Perl subroutine libraries into Bio.pl. One day in 1995, Steve Brenner, a Ph.D. student of Cyrus Chothia visited the room and started to discuss what they would call the perl library after some lengthy (a few months) debate on whether Perl is superior to C for bioinformatics as Steve Brenner had his own C library for bioinformatics. The two Ph.D. students named the net Perl library for biology Bioperl after going through names such as protein perl, protperl, PerlBio, and so on. Steve Brenner organized a Bioperl session in 1995 at ISMB Cambridge although it did not really happen. Bioperl had some users in coming months including Georg Fuellen who organized a training course in Germany. Georg's colleagues and students extended the Bioperl much and this was joined later by other people such as Steve Chervitz who was actively developing Perl codes for his yeast genome DB. The major expansion came when another Cambridge student Ewan Birney joined the wagon after another lengthy debate on if Perl was superior to C for bioinformatics and Ewan and many other people were very active in developing Bioperl.[citation needed]

The first stable release was on 11 June 2002; the most recent stable (in terms of API) release is 1.6.9 from 14 April 2011. There are also developer releases produced periodically. Version series 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.

Features

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

Usage

In addition to being used directly by end-users,[4] BioPerl has also provided the base for a wide variety of bioinformatic tools, including amongst others:

  • SynBrowse [5]
  • GeneComber [6]
  • TFBS [7]
  • MIMOX [8]
  • BioParser [9]
  • Degenerate primer design [10]
  • Querying the public databases [11]
  • Current Comparative Table [12]

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

  • Dealing with phylogenetic trees and nested taxa [13]
  • FPC Web tools [14]

Related Programming Languages

Several related bioinformatics programming languages exist as part of the Open Bioinformatics Foundation including:

References

  1. ↑ Stajich, J. E.; Block, D.; Boulez, K.; Brenner, S.; Chervitz, S.; Dagdigian, C.; Fuellen, G.; Gilbert, J.; Korf, I.; Lapp, H.; Lehväslaiho, H.; Matsalla, C.; Mungall, C. J.; Osborne, B. I.; Pocock, M. R.; Schattner, P.; Senger, M.; Stein, L. D.; Stupka, E.; Wilkinson, M. D.; Birney, E. (2002). "The BioPerl Toolkit: Perl Modules for the Life Sciences". Genome Research 12 (10): 1611–1618. doi:10.1101/gr.361602. PMC 187536. PMID 12368254. 
  2. ↑ http://www.bioperl.org/wiki/BioPerl_publications A complete, up-to-date list of BioPerl references
  3. ↑ Lincoln Stein (1996). "How Perl saved the human genome project". The Perl Journal 1 (2). Retrieved 2009-02-25 (Bioperl.org). 
  4. ↑ 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. 
  5. ↑ Pan, X.; Stein, L.; Brendel, V. (2005). "SynBrowse: A synteny browser for comparative sequence analysis". Bioinformatics 21 (17): 3461–3468. doi:10.1093/bioinformatics/bti555. PMID 15994196. 
  6. ↑ Shah, S. P.; McVicker, G. P.; MacKworth, A. K.; Rogic, S.; Ouellette, B. F. F. (2003). "GeneComber: Combining outputs of gene prediction programs for improved results". Bioinformatics 19 (10): 1296–1297. doi:10.1093/bioinformatics/btg139. PMID 12835277. 
  7. ↑ Lenhard, B.; Wasserman, W. W. (2002). "TFBS: Computational framework for transcription factor binding site analysis". Bioinformatics 18 (8): 1135–1136. doi:10.1093/bioinformatics/18.8.1135. PMID 12176838. 
  8. ↑ 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. 
  9. ↑ Catanho, M.; Mascarenhas, D.; Degrave, W.; De Miranda, A. B. ?L. (2006). "BioParser". Applied Bioinformatics 5 (1): 49–53. doi:10.2165/00822942-200605010-00007. PMID 16539538. 
  10. ↑ Wei, X.; Kuhn, D. N.; Narasimhan, G. (2003). "Degenerate primer design via clustering". Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference 2: 75–83. PMID 16452781. 
  11. ↑ Croce, O.; Lamarre, M. L.; 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. 
  12. ↑ Landsteiner, B. R.; Olson, M. R.; Rutherford, R. (2005). "Current Comparative Table (CCT) automates customized searches of dynamic biological databases". Nucleic Acids Research 33 (Web Server issue): W770–W773. doi:10.1093/nar/gki432. PMC 1160193. PMID 15980582. 
  13. ↑ Llabrés, M.; Rocha, J.; Rosselló, F.; Valiente, G. (2006). "On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa". Journal of Mathematical Biology 53 (3): 340–364. doi:10.1007/s00285-006-0011-4. PMID 16823581. 
  14. ↑ Pampanwar, V.; Engler, F.; Hatfield, J.; Blundy, S.; Gupta, G.; Soderlund, C. (2005). "FPC Web Tools for Rice, Maize, and Distribution". Plant Physiology 138 (1): 116–126. doi:10.1104/pp.104.056291. PMC 1104167. PMID 15888684. 
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