Provided by: libtfbs-perl_0.7.1-2_amd64
TFBS::PatternGen::Gibbs - a pattern factory that uses Chip Lawrences Gibbs program
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
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.