Bio::Tools::Run::PiseApplication::diffseq(3)

NAME
Bio::Tools::Run::PiseApplication::diffseq

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::diffseq

      Bioperl class for:

        DIFFSEQ Find differences between nearly identical sequences (EMBOSS)

      Parameters:

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

                diffseq (String)

                init (String)

                asequence (Sequence)
                        asequence -- any [single sequence] (-asequence)
                        pipe: seqfile

                bsequence (Sequence)
                        bsequence [single sequence] (-bsequence)

                wordsize (Integer)
                        Word size (-wordsize)

                outfile (OutFile)
                        Output report file (-outfile)

                afeatout (OutFile)
                        Feature file for output asequence (-afeatout)

                afeatout_offormat (Excl)
                        Feature output format (-offormat)

                bfeatout (OutFile)
                        Feature file for output bsequence (-bfeatout)

                bfeatout_offormat (Excl)
                        Feature output format (-offormat)

                columns (Switch)
                        Output in columns format (-columns)

                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 the web:

  http://bugzilla.bioperl.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/diffseq.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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