NAME

Bio::Tools::Run::PiseApplication::protal2dna

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::protal2dna

      Bioperl class for:

        protal2dna      Align DNA sequences corresponding to a protein    alignment (K. Schuerer, C. Letondal)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/protal2dna.html 
         for available values):


                protal2dna (String)

                outfile (OutFile)
                        pipe: readseq_ok_alig

                alig (Sequence)
                        Protein alignment
                        pipe: readseq_ok_alig

                dna (Sequence)
                        DNA Sequences File

                fasta (String)

                same_ids (Switch)
                        Identify corresponding DNA sequences by same ID or name (-i)

                outformat (Excl)
                        Output Alignment Format

                genetic (Excl)
                        Default Genetic Code (-g)

                speccode (InFile)
                        Special Genetic Code (-G)

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/protal2dna.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

 Title   : new()
 Usage   : my $protal2dna = Bio::Tools::Run::PiseApplication::protal2dna->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::protal2dna 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 $protal2dna = $factory->program('protal2dna');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::protal2dna.