Bio::Tools::Run::PiseApplication::satellites # 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)

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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/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.