Bio::Tools::Run::PiseApplication::restover(3)

NAME
Bio::Tools::Run::PiseApplication::restover

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::restover

      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)

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/MailList.shtml  - 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.bioperl.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/restover.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

  new
 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.