Bio::Tools::Run::PiseApplication::pima # Bio::Tools::Run::PiseApplication::pima Bioperl class for: PIMA Pattern-Induced Multi-sequence Alignment program (R. D. Smith and T. F. Smith) References: R. D. Smith and T. F. Smith. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative modelling. protein Engineering, vol5, number 1, pp 35-41, 1992 Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/pima.html for available values): pima (String) sequence (Sequence) Sequences cluster_name (String) cluster_name ref_seq_name (String) ref_seq_name sec_struc_seq_filename (InFile) sec_struc_seq_filename score_cutoff (Float) cluster score cutoff (-c) ext_gap_cost (Integer) gap extension penalty (-d) gap_open_cost (Integer) gap opening penalty (-i) min_score (Integer) minimum local score (-l) mat_file (InFile) matrix file (-m) not_num_ext (Switch) Do not use numerical extensions on each step of the alignment. (-n) sec_struc_gap_cost (Integer) secondary structure gap penalty (-t)

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

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