NAME

Bio::Tools::Run::PiseApplication::showseq

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::showseq

      Bioperl class for:

        SHOWSEQ Display a sequence with features, translation etc.. (EMBOSS)


      Parameters: 

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


                showseq (String)

                init (String)

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

                format (Excl)
                        Display format -- Things to display (-format)

                things (List)
                        Enter a list of things to display -- Specify your own things to display [select  values] (-things)

                translate (Integer)
                        Regions to translate (eg: 4-57,78-94) (-translate)

                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)

                annotation (Integer)
                        Regions to mark (eg: 4-57 promoter region 78-94 first exon) (-annotation)

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

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

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

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

                single (Switch)
                        Force single RE site only cuts (-single)

                blunt (Switch)
                        Allow blunt end RE cutters (-blunt)

                sticky (Switch)
                        Allow sticky end RE cutters (-sticky)

                ambiguity (Switch)
                        Allow ambiguous RE matches (-ambiguity)

                plasmid (Switch)
                        Allow circular DNA (-plasmid)

                commercial (Switch)
                        Only use restriction enzymes with suppliers (-commercial)

                limit (Switch)
                        Limits RE hits to one isoschizomer (-limit)

                preferred (Switch)
                        Report preferred isoschizomers (-preferred)

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

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

                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)
                        Show sequence ID (-name)

                description (Switch)
                        Show description (-description)

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

                html (Switch)
                        Use HTML formatting (-html)

                matchsource (String)
                        Source of feature to display (-matchsource)

                matchtype (String)
                        Type of feature to display (-matchtype)

                matchsense (Integer)
                        Sense of feature to display (-matchsense)

                minscore (Float)
                        Minimum score of feature to display (-minscore)

                maxscore (Float)
                        Maximum score of feature to display (-maxscore)

                matchtag (String)
                        Tag of feature to display (-matchtag)

                matchvalue (String)
                        Value of feature tags to display (-matchvalue)

                outfile (OutFile)
                        Output sequence details to a file (-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/showseq.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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