BioPerl

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. It is an open source software project which is still under active development. The first stable release was on June 11 2002, the most recent stable (in terms of API) release is 1.4.0 from December 2003. There are also unstable developer releases produced periodically, the most recent being 1.5.2 from December 62006. 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.

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Benefits

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

• Accessing 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, ^[2] BioPerl has also provided the base for a wide variety of bioinformatic tools, including amongst others:

• SynBrowse ^[3]
• GeneComber ^[4]
• TFBS ^[5]
• MIMOX ^[6]
• BioParser ^[7]
• Degenerate primer design ^[8]
• Querying the public databases ^[9]
• Current Comparative Table ^[10]

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

• Dealing with phylogenetic trees and nested taxa ^[11]
• FPC Web tools ^[12]

See also

• Open Bioinformatics Foundation
• BioPerl.org
• A tutorial for using BioPerl
• HOWTO documents for using BioPerl

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. 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. 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. PMID 12835277.
5. ^ Lenhard B, Wasserman W (2002). "TFBS: Computational framework for transcription factor binding site analysis". Bioinformatics 18 (8): 1135-6. 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. 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. 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. PMID 15888684.