Bio::Tools::Run::PiseApplication::assp # Bio::Tools::Run::PiseApplication::assp Bioperl class for: ASSP Accuracy of Secondary Structure Prediction (Russell, Barton) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/assp.html for available values): assp (String) aligfile (InFile) Alignement File (in BLOCK format) clus2blc (Switch) Convert CLUSTAL NBRF-PIR format to AMPS Blockfile format nbrf_file (String) showpar (Switch) show all the parameters for the current run. quiet (Switch) avoid all output in the program except for errors and a final lower limit for Q3 matrix (InFile) -m property type matrix file name subsize (Integer) -s length of sequence used to determine poor alignment maxalig (Integer) -l maximum number of sub-alignments to be considered minprop (Integer) -p minimum number or properties shared to define conservation window (Integer) -w window length for conservation definition ignseq (Integer) -i fraction of sequences that may be ignored mingap (Integer) -g minimum number of gaps allowed seqomit (String) -o Seq. to be omitted 1 Seq. to be omitted 2 ...

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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/assp.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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