NAME

Bio::Tools::Run::PiseApplication::msbar

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::msbar

      Bioperl class for:

        MSBAR   Mutate sequence beyond all recognition (EMBOSS)


      Parameters: 

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


                msbar (String)

                init (String)

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

                count (Integer)
                        Number of times to perform the mutation operations (-count)

                point (List)
                        Types of point mutations to perform -- Point mutation operations [select  values] (-point)

                block (List)
                        Types of block mutations to perform -- Block mutation operations [select  values] (-block)

                inframe (Switch)
                        Do 'codon' and 'block' operations in frame (-inframe)

                codon (List)
                        Types of codon mutations to perform -- Codon mutation operations [select  values] (-codon)

                minimum (Integer)
                        Minimum size for a block mutation (-minimum)

                maximum (Integer)
                        Maximum size for a block mutation (-maximum)

                other (Sequence)
                        Other sequences that the mutated result should not match (-other)

                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/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/msbar.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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