NAME

Bio::Tools::Run::PiseApplication::mreps

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::mreps

      Bioperl class for:

        mreps   Algorithm for finding maximal tandem repetitions (G. Kucherov)

        References:

                R. Kolpakov, G. Kucherov, Finding maximal repetitions in a word in linear time, 1999 Symposium on Foundations of Computer Science (FOCS), New-York (USA), pp. 596-604, IEEE Computer Society 

                R. Kolpakov, G. Kucherov, Finding Approximate Repetitions under Hamming Distance, 9-th European Symposium on Algorithms (ESA), Århus (Denmark), Lecture Notes in Computer Science, vol. 2161, pp 170-181.



      Parameters: 

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


                mreps (String)

                query (Sequence)
                        Query Sequence file

                err (Integer)
                        Specifies the resolution (error level) (-res)

                from (Integer)
                        Specifies starting position (-from)

                to (Integer)
                        Specifies end position (-to)

                win (Integer)
                        Processes by sliding windows of size 2*n overlaping by n (-win)

                minsize (Integer)
                        Report repetitions whose size is at least n (-minsize)

                maxsize (Integer)
                        Report repetitions whose size is at most n (-maxsize)

                minperiod (Integer)
                        Report repetitions whose period is at least n (-minperiod)

                maxperiod (Integer)
                        Report repetitions whose period is at most n (-maxperiod)

                exp (Integer)
                        Report repetitions whose exponent is at least n (-exp)

                small (Switch)
                        Output small repeats that can occur randomly (-allowsmall)

                noprint (Switch)
                        Do not output repetitions sequences (-noprint)

                xml (OutFile)
                        XML format output file name (-xmloutput)

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/mreps.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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