NAME

Bio::Tools::Run::PiseApplication::satellites

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::satellites

      Bioperl class for:

        satellites      identifying satellites and periodic repetitions in biological sequence s (constrained version) (MF. Sagot, G. Myers, E. Poiret)


      Parameters: 

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


                satellites (String)

                seq (Sequence)
                        Sequence File

                alphabet (Excl)
                        Alphabets and score system (-a)

                outputbase (String)

                scoreN (String)

                maxsym (String)

                range (String)

                gap (Integer)

                minlen (Integer)
                        Minimum length of repeats (minlen)

                maxlen (Integer)
                        Maximum length of repeats (maxlen)

                maxerr (Integer)
                        Maximum number of errors allowed between each repeat and the model for a satellite (not more than 10% of the model length) (maxerr)

                indel (Switch)
                        Insertions and deletions allowed (indel)

                maxjump (Integer)
                        Maximum number of 'bad' repeats between 2 'good' ones (not more than 5) (maxjump)

                quorum (Integer)
                        Minimum number of repeats a satellite must have (quorum)

                usematrix (Switch)
                        Use scores instead of matrix (usematrix)

                scorematch (Integer)
                        Score attributed to a match for the final scoring of a model (scorematch)

                scoresub (Integer)
                        Score attributed to a substitution for the final scoring of a model (scoresub)

                scoregap (Integer)
                        Score attributed to an indel for the final scoring of a model (scoregap)

                threshold (Integer)
                        Filter threshold (threshold)

                threscore (Integer)
                        Print threshold (i.e minimum score for printing a model) (threscore)

                inverted (Switch)
                        Inverted occurences allowed (inverted)

                ngroup (String)

                xml (Switch)
                        XML output (xml)

                xmldtdcopy (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/satellites.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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