NAME

       TFBS::PatternGen::Gibbs - a pattern factory that uses Chip Lawrences Gibbs program

SYNOPSIS

           my $patterngen =
                   TFBS::PatternGen::Gibbs->new(-seq_file=>'sequences.fa',
                                                -binary => '/Programs/Gibbs-1.0/bin/Gibbs'
                                                -nr_hits => 24,
                                                -motif_length => [8, 9, 10],
                                                -additional_params => '-x -r -e');

           my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object

DESCRIPTION

       TFBS::PatternGen::Gibbs builds position frequency matrices using an advanced Gibbs
       sampling algorithm implemented in external Gibbs program by Chip Lawrence. The algorithm
       can produce multiple patterns from a single set of sequences.

   new
        Title   : new
        Usage   : my $db = TFBS::PatternGen::Gibbs->new(%args);
        Function: the constructor for the TFBS::PatternGen::Gibbs object
        Returns : a TFBS::PatternGen::Gibbs object
        Args    : This method takes named arguments;
                   you must specify one of the following three
                   -seq_list     # a reference to an array of strings
                                 #   and/or Bio::Seq objects
                     # or
                   -seq_stream   # A Bio::SeqIO object
                     # or
                   -seq_file     # the name of the fasta file containing
                                 #   all the sequences
                  Other arguments are:
                   -binary       # a fully qualified path to Gibbs executable
                                 #  OPTIONAL: default 'Gibbs'
                   -nr_hits      # a presumed number of pattern occurrences in the
                                 #   sequence set: it can be a single integer, e.g.
                                 #   -nr_hits => 24 , or a reference to an array of
                                 #   integers, e.g -nr_hits => [12, 24, 36]
                   -motif_length # an expected length of motif in nucleotides:
                                 #   it can be a single integer, e.g.
                                 #   -motif_length => 8 , or a reference to an
                                 #   array ofintegers, e.g -motif_length => [8..12]
                   -additional_params  # a string containing additional
                                       #   command-line switches for the
                                       #   Gibbs program

   pattern
   all_patterns
   patternSet
       The three methods listed above are used for the retrieval of patterns, and are common to
       all TFBS::PatternGen::* classes. Please see TFBS::PatternGen for details.