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NAME

Bio::Tools::Run::PiseApplication::consensus

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::consensus

      Bioperl class for:

        CONSENSUS       Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo)

        References:

                G.Z. Hertz and G.D. Stormo.  Identification of consensus patterns in unaligned DNA and protein sequences: a large-deviation statistical basis for penalizing gaps. In: Proceedings of the Third International Conference on Bioinformatics and Genome Research (H.A. Lim, and C.R. Cantor, editors). World Scientific Publishing Co., Ltd. Singapore, 1995. pages 201--216.



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/consensus.html 
         for available values):


                consensus (Excl)
                        Program to run

                sequence (Sequence)
                        Sequences file (-f)
                        pipe: seqsfile

                width (Integer)
                        Width of pattern (consensus only) (-L)

                out (String)

                consensus_matrix (String)

                complement (Excl)
                        Complement of nucleic acid sequences (-c)

                ascii_alphabet (InFile)
                        Alphabet and normalization information (if not DNA) (-a)

                prior (Switch)
                        Use the designated prior probabilities of the letters to override the observed frequencies (-d)

                dna (Switch)
                        Alphabet and normalization information for DNA

                protein (Switch)
                        Alphabet and normalization information for protein

                queue (Integer)
                        Maximum number of matrices to save between cycles of the program -- ie: queue size (-q)

                standard_deviation (Float)
                        Number of standard deviations to lower the information content at each position before identifying information peaks (mandatory for wconsensus) (-s)

                progeny (Excl)
                        Save the top progeny matrices  (-pr1)

                linearly (Switch)
                        Seed with the first sequence and proceed linearly through the list (-l)

                max_cycle_nb (Integer)
                        Maximum repeat of the matrix building cycle (-n or -N)

                max_cycle (Excl)
                        How many words per matrix for each sequence to contribute (-n or -N)

                distance (Integer)
                        Minimum distance between the starting points of words within the same matrix pattern (-m)

                terminate (Integer)
                        Terminate the program this number of cycles after the current most significant alignment is identified (-t)

                terminal_gap (Excl)
                        Permit terminal gaps (-pg) (wconsensus only)

                top_matrices (Integer)
                        Number of top matrices to print (-pt)

                final_matrices (Integer)
                        Number of final matrices to print (-pf)

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/consensus.html

  • Bio::Tools::Run::PiseApplication

  • Bio::Tools::Run::AnalysisFactory::Pise

  • Bio::Tools::Run::PiseJob

new

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