Bio::Tools::Run::PiseApplication::align2model # Bio::Tools::Run::PiseApplication::align2model Bioperl class for: SAM align2model - create a multiple alignment of sequences to an existing model (R. Hughey, A. Krogh) References: R. Hughey and A. Krogh., SAM: Sequence alignment and modeling software system. Technical Report UCSC-CRL-96-22, University of California, Santa Cruz, CA, September 1996. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/align2model.html for available values): align2model (String) run (String) Run name db (Sequence) Sequences to align (-db) model_file (InFile) Model (-i) pipe: sam_model id (String) Sequence identifier(s) selection (separated by commas) (-id) nscoreseq (Integer) Maximum number of sequences to be read (-nscoreseq) adpstyle (Excl) Dynamic programming style (-adpstyle SW (Excl) Sequence scoring (-SW) auto_fim (Switch) Add FIMs automatically (-auto_fim) jump_in_prob (Float) Probability cost of jumping into the center of the model (-jump_in_prob) jump_out_prob (Float) Probability cost of jumping out the center of the model (-jump_out_prob) a2mdots (Switch) Print dots to fill space need for other sequences' insertions (-a2mdots) dump_parameters (Excl) (-dump_parameters)

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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/align2model.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

new
Title : new() Usage : my $align2model = Bio::Tools::Run::PiseApplication::align2model->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::align2model 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 $align2model = $factory->program('align2model'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::align2model.