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Bio::Tools::Run::PiseApplication::align2model.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::align2modelSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::align2modelBioperl 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)
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/align2model.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 $align2model = Bio::Tools::Run::PiseApplication::align2model->new($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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre