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Bio::Tools::Run::PiseApplication::est2genome.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::est2genomeSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::est2genomeBioperl class for: EST2GENOME Align EST and genomic DNA sequences (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/est2genome.html for available values): est2genome (String) init (String) est (Sequence) EST sequence(s) (-est) pipe: seqsfile genome (Sequence) Genomic sequence (-genome) pipe: seqfile match (Integer) Score for matching two bases (-match) mismatch (Integer) Cost for mismatching two bases (-mismatch) gappenalty (Integer) Gap penalty (-gappenalty) intronpenalty (Integer) Intron penalty (-intronpenalty) splicepenalty (Integer) Splice site penalty (-splicepenalty) minscore (Integer) Minimum accepted score (-minscore) reverse (Switch) Reverse orientation (-reverse) splice (Switch) Use donor and acceptor splice sites (-splice) mode (String) Comparison mode (-mode) best (Switch) Print out only best alignment (-best) space (Float) Space threshold (in megabytes) (-space) shuffle (Integer) Shuffle (-shuffle) seed (Integer) Random number seed (-seed) outfile (OutFile) outfile (-outfile) align (Switch) Show the alignment (-align) width (Integer) Alignment width (-width) auto (String)
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/est2genome.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 $est2genome = Bio::Tools::Run::PiseApplication::est2genome->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::est2genome 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 $est2genome = $factory->program('est2genome'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::est2genome.
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