NAME

Bio::Tools::Run::PiseApplication::restrict

SYNOPSIS

#

DESCRIPTION

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)

FEEDBACK

Mailing Lists

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

Reporting Bugs

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/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

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.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

• http://bioweb.pasteur.fr/seqanal/interfaces/restrict.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

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.