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Bio::Tools::Run::PiseApplication::grailclnt.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::grailclntSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::grailclntBioperl 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
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.open-bio.org/
AUTHOR
Catherine Letondal (letondal@pasteur.fr)COPYRIGHT
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.
DISCLAIMER
This software is provided ``as is'' without warranty of any kind.SEE ALSO
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- http://bioweb.pasteur.fr/seqanal/interfaces/grailclnt.html
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- Bio::Tools::Run::PiseApplication
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- Bio::Tools::Run::AnalysisFactory::Pise
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- 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.
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