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BioPerl [1] is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. NOTES FOR EDITORS "Perl" is not an acronym (read the "Name" section below Bioinformatics is the application of information technology to the field of molecular biology It has played an integral role in the Human Genome Project. The Human Genome Project (HGP was an international Scientific research project with a primary goal to determine the sequence of chemical base pairs which make up DNA It is an open source software project which is still under active development. Open source is a development methodology which offers practical accessibility to a product's source (goods and knowledge The first stable release was on June 11, 2002, the most recent stable (in terms of API) release is 1. Events 1184 BC - Trojan War: Troy is sacked and burned according to the calculations of Eratosthenes. See also 2002 (disambiguation Year 2002 ( MMII) was a Common year starting on Tuesday of the Gregorian calendar. 4. 0 from December 2003. Year 2003 ( MMIII) was a Common year starting on Wednesday of the Gregorian calendar. There are also unstable developer releases produced periodically, the most recent being 1.5.2 from December 6, 2006. Events 1060 - Béla I of Hungary is crowned king of Hungary 1240 - Mongol invasion of Rus: Kiev Year 2006 ( MMVI) was a Common year starting on Sunday of the Gregorian calendar. Version 1. 5. 2 is considered to be the most stable (in terms of bugs) version of BioPerl and believed to be suitable for most peoples requirements.

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

Benefits

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, [2] 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:

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). In Bioinformatics, a sequence alignment is a way of arranging the Primary sequences of DNA, RNA, or Protein to identify regions of The Open Bioinformatics Foundation is a Non profit, volunteer run organization focused on supporting Open source Programming in Bioinformatics "The Bioperl toolkit: Perl modules for the life sciences". Genome Res 12 (10): 1611-8. doi:10.1101/gr.361602. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document. PMID 12368254.  
  2. ^ Khaja R, MacDonald J, Zhang J, Scherer S. "Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes". Methods Mol Biol 338: 9-20. PMID 16888347.  
  3. ^ 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. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document. PMID 15994196.  
  4. ^ 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. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document. PMID 12835277.  
  5. ^ 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. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document. PMID 12176838.  
  6. ^ Huang J, Gutteridge A, Honda W, Kanehisa M. "MIMOX: a web tool for phage display based epitope mapping". BMC Bioinformatics 7: 451. PMID 17038191.  
  7. ^ 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. PMID 16539538.  
  8. ^ Wei X, Kuhn D, Narasimhan G. "Degenerate primer design via clustering". Proc IEEE Comput Soc Bioinform Conf 2: 75-83. PMID 16452781.  
  9. ^ Croce O, Lamarre M, Christen R. "Querying the public databases for sequences using complex keywords contained in the feature lines". BMC Bioinformatics 7: 45. PMID 16441875.  
  10. ^ 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. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document. PMID 15980582.  
  11. ^ 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. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document. PMID 16823581.  
  12. ^ 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. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document. PMID 15888684.  
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