Bio::Tools::Run::PiseApplication::trnascan(3)

NAME
Bio::Tools::Run::PiseApplication::trnascan

SYNOPSIS
  #

DESCRIPTION
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)

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/MailList.shtml  - 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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

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

•   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.