- BioPerl
BioPerl [cite journal |author=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 |title=The Bioperl toolkit: Perl modules for the life sciences |journal=Genome Res |volume=12 |issue=10 |pages=1611–8 |year=2002 |pmid=12368254 |doi=10.1101/gr.361602] is a collection of
Perl modules that facilitate the development of Perl scripts forbioinformatics applications. It has played an [http://www.bioperl.org/wiki/How_Perl_saved_human_genome integral role] in theHuman Genome Project .It is anopen source software project which is still under active development. The first stable release was onJune 11 2002 , the most recent stable (in terms of API) release is 1.4.0 from December2003 . There are also unstable developer releases produced periodically, the most recent being [http://bioperl.org/wiki/Release_1.5.2 1.5.2] fromDecember 6 2006 . 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.
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 manipulatingsequence alignment s
* Searching for genes and other structures on genomic DNA
* Developing machine readable sequence annotationsUsage
In addition to being used directly by end-users, [cite journal |author=Khaja R, MacDonald J, Zhang J, Scherer S |title=Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes |journal=Methods Mol Biol |volume=338 |issue= |pages=9–20 |year= |pmid=16888347] BioPerl has also provided the base for a wide variety of bioinformatic tools, including [http://www.bioperl.org/wiki/BioPerl_publications amongst others] :
* SynBrowse [cite journal |author=Pan X, Stein L, Brendel V |title=SynBrowse: a synteny browser for comparative sequence analysis |journal=Bioinformatics |volume=21 |issue=17 |pages=3461–8 |year=2005 |pmid=15994196 |doi=10.1093/bioinformatics/bti555]
* GeneComber [cite journal |author=Shah S, McVicker G, Mackworth A, Rogic S, Ouellette B |title=GeneComber: combining outputs of gene prediction programs for improved results |journal=Bioinformatics |volume=19 |issue=10 |pages=1296–7 |year=2003 |pmid=12835277 |doi=10.1093/bioinformatics/btg139]
* TFBS [cite journal |author=Lenhard B, Wasserman W |title=TFBS: Computational framework for transcription factor binding site analysis |journal=Bioinformatics |volume=18 |issue=8 |pages=1135–6 |year=2002 |pmid=12176838 |doi=10.1093/bioinformatics/18.8.1135]
* MIMOX [cite journal |author=Huang J, Gutteridge A, Honda W, Kanehisa M |title=MIMOX: a web tool for phage display based epitope mapping |journal=BMC Bioinformatics |volume=7 |issue= |pages=451 |year= 2006|pmid=17038191 |doi=10.1186/1471-2105-7-451]
* BioParser [cite journal |author=Catanho M, Mascarenhas D, Degrave W, de Miranda A |title=BioParser: a tool for processing of sequence similarity analysis reports |journal=Appl Bioinformatics |volume=5 |issue=1 |pages=49–53 |year=2006 |pmid=16539538 |doi=10.2165/00822942-200605010-00007]
* Degenerate primer design [cite journal |author=Wei X, Kuhn D, Narasimhan G |title=Degenerate primer design via clustering |journal=Proc IEEE Comput Soc Bioinform Conf |volume=2 |issue= |pages=75–83 |year= |pmid=16452781]
* Querying the public databases [cite journal |author=Croce O, Lamarre M, Christen R |title=Querying the public databases for sequences using complex keywords contained in the feature lines |journal=BMC Bioinformatics |volume=7 |issue= |pages=45 |year= 2006|pmid=16441875 |doi=10.1186/1471-2105-7-45]
* Current Comparative Table [cite journal |author=Landsteiner B, Olson M, Rutherford R |title=Current Comparative Table (CCT) automates customized searches of dynamic biological databases |journal=Nucleic Acids Res |volume=33 |issue=Web Server issue |pages=W770–3 |year=2005 |pmid=15980582 |doi=10.1093/nar/gki432]New tools and algorithms from external developers are often integrated directly into BioPerl itself:
* Dealing with phylogenetic trees and nested taxa [cite journal |author=Llabrés M, Rocha J, Rosselló F, Valiente G |title=On the ancestral compatibility of two phylogenetic trees with nested taxa |journal=J Math Biol |volume=53 |issue=3 |pages=340–64 |year=2006 |pmid=16823581 |doi=10.1007/s00285-006-0011-4]
* FPC Web tools [cite journal |author=Pampanwar V, Engler F, Hatfield J, Blundy S, Gupta G, Soderlund C |title=FPC Web tools for rice, maize, and distribution |journal=Plant Physiol |volume=138 |issue=1 |pages=116–26 |year=2005 |pmid=15888684 |doi=10.1104/pp.104.056291]ee also
*
Open Bioinformatics Foundation
* [http://bioperl.org BioPerl.org]
* A [http://bioperl.org/wiki/Bptutorial.pl tutorial] for using BioPerl
* [http://bioperl.org/wiki/HOWTOs HOWTO] documents for using BioPerlReferences
For a complete, up-to-date list of Bioperl references, please see [http://www.bioperl.org/wiki/BioPerl_publications BioPerl publications]
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