TFBS::PatternGen::Gibbs(3pm)
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 occurences 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.