World Library  
Flag as Inappropriate
Email this Article

BioPerl

Article Id: WHEBN0000559864
Reproduction Date:

Title: BioPerl  
Author: World Heritage Encyclopedia
Language: English
Subject: BioJava, .NET Bio, Perl, Biopython, Bioinformatics
Collection: Bioinformatics, Bioinformatics Software, Free Bioinformatics Software, Perl Software
Publisher: World Heritage Encyclopedia
Publication
Date:
 

BioPerl

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 .orgbioperl

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]

Contents

  • Background 1
  • Features 2
  • Usage 3
  • Related Libraries in Other Programming Languages 4
  • References 5

Background

BioPerl is an active 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.

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:

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 Libraries in Other Programming Languages

Several related bioinformatics libraries implemented in other programming languages exist as part of the Open Bioinformatics Foundation including:

References

  1. ^ Stajich, J. E.; Block, D.; Boulez, K.;  
  2. ^ http://www.bioperl.org/articles/BioPerl_publications A complete, up-to-date list of BioPerl references
  3. ^  
  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.  
  5. ^ Pan, X.;  
  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.  
  7. ^ Lenhard, B.; Wasserman, W. W. (2002). "TFBS: Computational framework for transcription factor binding site analysis". Bioinformatics 18 (8): 1135–1136.  
  8. ^ Huang, J.; Gutteridge, A.; Honda, W.; Kanehisa, M. (2006). "MIMOX: A web tool for phage display based epitope mapping". BMC Bioinformatics 7: 451.  
  9. ^ Catanho, M.; Mascarenhas, D.; Degrave, W.; De Miranda, A. B. ?L. (2006). "BioParser". Applied Bioinformatics 5 (1): 49–53.  
  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.  
  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.  
  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.  
  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.  
  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.  
This article was sourced from Creative Commons Attribution-ShareAlike License; additional terms may apply. World Heritage Encyclopedia content is assembled from numerous content providers, Open Access Publishing, and in compliance with The Fair Access to Science and Technology Research Act (FASTR), Wikimedia Foundation, Inc., Public Library of Science, The Encyclopedia of Life, Open Book Publishers (OBP), PubMed, U.S. National Library of Medicine, National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health (NIH), U.S. Department of Health & Human Services, and USA.gov, which sources content from all federal, state, local, tribal, and territorial government publication portals (.gov, .mil, .edu). Funding for USA.gov and content contributors is made possible from the U.S. Congress, E-Government Act of 2002.
 
Crowd sourced content that is contributed to World Heritage Encyclopedia is peer reviewed and edited by our editorial staff to ensure quality scholarly research articles.
 
By using this site, you agree to the Terms of Use and Privacy Policy. World Heritage Encyclopedia™ is a registered trademark of the World Public Library Association, a non-profit organization.
 


Copyright © World Library Foundation. All rights reserved. eBooks from Project Gutenberg are sponsored by the World Library Foundation,
a 501c(4) Member's Support Non-Profit Organization, and is NOT affiliated with any governmental agency or department.