NAME

Bio::Tools::Run::PiseApplication::cds

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::cds

      Bioperl class for:

        CDS     Search Coding Regions (F. Chauveau)


      Parameters: 

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


                cds (String)

                seq (Sequence)
                        Sequence File

                minaa (Integer)
                        Minimum number of amino acids in CDS

                frame (Excl)
                        Frame

                starts (String)
                        START codons (separated by commas)

                maxf (Switch)
                        longest CDS in each frame

                max (Switch)
                        longest CDS

                all (Switch)
                        all CDS, including CDS inside CDS

                nucl (Switch)
                        nucleotids output

                print_adn (Switch)
                        Print ADN as well as Amino-acids

                left_adn (Integer)
                        How many base pairs on the left (if print ADN)

                print_frame (Switch)
                        print frame before search

                print_pos (Switch)
                        print only position(s)

                xml (Switch)
                        XML output (-x)

                xmldtdcopy (String)

                end_stop (Switch)
                        CDS ends at STOP

                genetic (Excl)
                        Genetic Code

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/cds.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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