Bio::Tools::Run::PiseApplication::trnascan # Bio::Tools::Run::PiseApplication::trnascan Bioperl class for: tRNAscan-SE detection of transfer RNA genes (T. Lowe, S. Eddy) References: Fichant, G.A. and Burks, C. (1991) Identifying potential tRNA genes in genomic DNA sequences, J. Mol. Biol., 220, 659-671. Eddy, S.R. and Durbin, R. (1994) RNA sequence analysis using covariance models, Nucl. Acids Res., 22, 2079-2088. Pavesi, A., Conterio, F., Bolchi, A., Dieci, G., Ottonello, S. (1994) Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of trnascriptional control regions, Nucl. Acids Res., 22, 1247-1256. Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence, Nucl. Acids Res., 25, 955-964. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/trnascan.html for available values): trnascan (String) sequence (Sequence) Sequence File prokaryotic (Switch) Improve detection of prokaryotic tRNAs (-P) archeal (Switch) Select archeal-specific covariance model (-A) organellar (Switch) Bypasses the fast first-pass scanners that are poor at detecting organellar tRNAs (-O) general (Switch) general covariance model trained on all three phylogenetic domains (-G) cove_only (Switch) Analyze sequences using Cove only (-C) trnascan_only (Switch) Use tRNAscan only to analyze sequences (-T) eufindtrna_only (Switch) Use EufindtRNA only to search for tRNAs (-E) trnascan_mode (Excl) Strict or relaxed tRNAscan mode (-t) eufindtrna_mode (Excl) EufindtRNA mode (-e) matching (String) Search only sequences with names matching this string (-n) start (String) Start search at first sequence with name matching this string (-s) genetic (Excl) Genetic code (-g) disable_checking (Switch) Manually disable checking tRNAs for poor primary or secondary structure scores often indicative of eukaryotic pseudogenes (-D) add_to_both_ends (Integer) Number of nucleotids to add to both ends during first-pass (-B cutoff (Integer) Cove cutoff score for reporting tRNAs (-X) length (Integer) Max length of tRNA intron+variable region (-L) previous_first_pass_result (InFile) Use a previous first pass result tabular file (-u) statistics (Switch) Save statistics summary for run (-m) secondary_structure (Switch) Save secondary structure results file (-f) save_first_pass (Switch) Save first pass results (-r) false_positives (Switch) Save false positives (-F) progress (Switch) Display program progress (-d) brief (Switch) Use brief output format (-b) quiet (Switch) Quiet mode (-q) acedb (Switch) Output final results in ACeDB format instead of the default tabular format (-a) trna_codon (Switch) Output a tRNA's corresponding codon in place of its anticodon (-N) scanners (Switch) Displays which of the first-pass scanners detected the tRNA being output (-y) unfinished_sequences (Switch) skip over N's in unfinished sequence (-i) breakdown (Switch) Display the breakdown of the two components of the bit score (-H)

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

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