TFBS::PatternGen::Gibbs(3) 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.

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