Bio::Tools::Run::PiseApplication::grailclnt # Bio::Tools::Run::PiseApplication::grailclnt Bioperl class for: GRAILCLNT Grail client (Xu, Einstein, Mural, Shah, Uberbacher) References: Xu, Y., Einstein, J. R., Mural, R.J., Shah, M. and Uberbacher, E.C., (1994) An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequences, Published Presentation: The Second International Conference on Intelligent Systems for Molecular Biology, Stanford University, San Francisco, CA, August 14-17, 1994. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/grailclnt.html for available values): grailclnt (String) seq (Sequence) Sequence feature (Excl) Which feature? organism (Excl) Organism header (Switch) Header translation (Switch) Translation strandscores (Switch) Strandscores (grail1) shadowexons (Switch) Shadowexons (grail 1.a or grail2) clusters (Switch) Clusters (grail 2) cluster_file (InFile) grail2exons results file pipe: grail_cluster modelexon_translation (Switch) Gene model exons translation genemodel_translation (Switch) Entire gene models translation auto_strand (Switch) AUTO STRAND start_strand (Integer) AUTO STRAND start end_strand (Integer) AUTO STRAND end forward_strand (Switch) FORWARD_STRAND reverse_strand (Switch) REVERSE_STRAND grail2_file (InFile) grail2exons results file pipe: grail_cluster fserr_strand (Excl) Strand rpttv_organism (String) start_seq (String) end_seq (String) end_request (String) outfile (OutFile) Result file pipe: grail_cluster

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

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