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

NAME
Bio::Tools::Run::PiseApplication::remap

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::remap

      Bioperl class for:

        REMAP   Display a sequence with restriction cut sites, translation etc.. (EMBOSS)

      Parameters:

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/remap.html
         for available values):

                remap (String)

                init (String)

                sequence (Sequence)
                        sequence -- DNA [sequences] (-sequence)
                        pipe: seqsfile

                enzymes (String)
                        Comma separated enzyme list (-enzymes)

                sitelen (Integer)
                        Minimum recognition site length (-sitelen)

                mincuts (Integer)
                        Minimum cuts per RE (-mincuts)

                maxcuts (Integer)
                        Maximum cuts per RE (-maxcuts)

                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)

                table (Excl)
                        Code to use -- Genetic codes (-table)

                outfile (OutFile)
                        Output sequence details to a file (-outfile)

                cutlist (Switch)
                        List the enzymes that cut (-cutlist)

                flatreformat (Switch)
                        Display RE sites in flat format (-flatreformat)

                limit (Switch)
                        Limits reports to one isoschizomer (-limit)

                preferred (Switch)
                        Report preferred isoschizomers (-preferred)

                translation (Switch)
                        Display translation (-translation)

                reverse (Switch)
                        Display cut sites and translation of reverse sense (-reverse)

                orfminsize (Integer)
                        Minimum size of ORFs (-orfminsize)

                uppercase (Integer)
                        Regions to put in uppercase (eg: 4-57,78-94) (-uppercase)

                highlight (Integer)
                        Regions to colour in HTML (eg: 4-57 red 78-94 green) (-highlight)

                threeletter (Switch)
                        Display protein sequences in three-letter code (-threeletter)

                number (Switch)
                        Number the sequences (-number)

                width (Integer)
                        Width of sequence to display (-width)

                length (Integer)
                        Line length of page (0 for indefinite) (-length)

                margin (Integer)
                        Margin around sequence for numbering (-margin)

                name (Switch)
                        Display sequence ID (-name)

                description (Switch)
                        Display description (-description)

                offset (Integer)
                        Offset to start numbering the sequence from (-offset)

                html (Switch)
                        Use HTML formatting (-html)

                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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

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/remap.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

  new
 Title   : new()
 Usage   : my $remap = Bio::Tools::Run::PiseApplication::remap->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::remap 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 $remap = $factory->program('remap');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::remap.