Bio::Tools::Run::PiseApplication::restover
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Bioperl class for: RESTOVER Finds restriction enzymes that produce a specific overhang (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/restover.html for available values): restover (String) init (String) sequence (Sequence) sequence -- DNA [sequences] (-sequence) pipe: seqsfile seqcomp (String) Overlap sequence (-seqcomp) min (Integer) Minimum cuts per RE (-min) max (Integer) Maximum cuts per RE (-max) single (Switch) Force single site only cuts (-single) threeprime (Switch) 3' overhang? (else 5') e.g. BamHI has CTAG as a 5' overhang, and ApaI has CCGG as 3' overhang. (-threeprime) 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) html (Switch) Create HTML output (-html) 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)
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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/restover.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob
Title : new() Usage : my $restover = Bio::Tools::Run::PiseApplication::restover->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::restover 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 $restover = $factory->program('restover'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::restover.
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.