Bio::Tools::Run::PiseApplication::mreps # 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)

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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/ Catherine Letondal (letondal@pasteur.fr) 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. This software is provided "as is" without warranty of any kind. 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.