NAME

Bio::Tools::Run::PiseApplication::getorf

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::getorf

      Bioperl class for:

        GETORF  Finds and extracts open reading frames (ORFs) (EMBOSS)


      Parameters: 

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


                getorf (String)

                init (String)

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

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

                minsize (Integer)
                        Minimum nucleotide size of ORF to report (-minsize)

                find (Excl)
                        Type of output -- Type of sequence to output (-find)

                methionine (Switch)
                        Change initial START codons to Methionine (-methionine)

                circular (Switch)
                        Is the sequence circular (-circular)

                reverse (Switch)
                        Find ORFs in the reverse sequence (-reverse)

                flanking (Integer)
                        Number of flanking nucleotides to report (-flanking)

                outseq (OutFile)
                        outseq (-outseq)
                        pipe: seqsfile

                outseq_sformat (Excl)
                        Output format for: outseq

                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/getorf.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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