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      Bioperl class for:

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


                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.


        (see also:
         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)


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Catherine Letondal (


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.



  • Bio::Tools::Run::PiseApplication

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

  • Bio::Tools::Run::PiseJob


 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.