Bio::Tools::Run::PiseApplication::restrict
#
Bioperl class for: RESTRICT Finds restriction enzyme cleavage sites (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/restrict.html for available values): restrict (String) init (String) sequence (Sequence) sequence -- DNA [sequences] (-sequence) pipe: seqsfile sitelen (Integer) Minimum recognition site length (-sitelen) enzymes (String) Comma separated enzyme list (-enzymes) min (Integer) Minimum cuts per RE (-min) max (Integer) Maximum cuts per RE (-max) single (Switch) Force single site only cuts (-single) blunt (Switch) Allow blunt end cutters (-blunt) sticky (Switch) Allow sticky end cutters (-sticky) ambiguity (Switch) Allow ambiguous matches (-ambiguity) plasmid (Switch) Allow circular DNA (-plasmid) commercial (Switch) Only enzymes with suppliers (-commercial) datafile (String) Alternative RE data file (-datafile) limit (Switch) Limits reports to one isoschizomer (-limit) preferred (Switch) Report preferred isoschizomers (-preferred) alphabetic (Switch) Sort output alphabetically (-alphabetic) fragments (Switch) Show fragment lengths (-fragments) name (Switch) Show sequence name (-name) outfile (OutFile) outfile (-outfile) auto (String)
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
Catherine Letondal (letondal@pasteur.fr)
Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
This software is provided "as is" without warranty of any kind.
http://bioweb.pasteur.fr/seqanal/interfaces/restrict.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob
Title : new() Usage : my $restrict = Bio::Tools::Run::PiseApplication::restrict->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::restrict object. This method should not be used directly, but rather by a Bio::Tools::Run::AnalysisFactory::Pise instance. my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(); my $restrict = $factory->program('restrict'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::restrict.
To install Bio::Factory::EMBOSS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Factory::EMBOSS
CPAN shell
perl -MCPAN -e shell install Bio::Factory::EMBOSS
For more information on module installation, please visit the detailed CPAN module installation guide.