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.IX Title "TFBS::PatternGen::Gibbs 3pm"
.TH TFBS::PatternGen::Gibbs 3pm 2024-03-13 "perl v5.38.2" "User Contributed Perl Documentation"
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.SH NAME
TFBS::PatternGen::Gibbs \- a pattern factory that uses Chip Lawrences Gibbs program
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 6
\&    my $patterngen =
\&            TFBS::PatternGen::Gibbs\->new(\-seq_file=>\*(Aqsequences.fa\*(Aq,
\&                                         \-binary => \*(Aq/Programs/Gibbs\-1.0/bin/Gibbs\*(Aq
\&                                         \-nr_hits => 24,
\&                                         \-motif_length => [8, 9, 10],
\&                                         \-additional_params => \*(Aq\-x \-r \-e\*(Aq);
\&
\&    my $pfm = $patterngen\->pattern(); # $pfm is now a TFBS::Matrix::PFM object
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
TFBS::PatternGen::Gibbs builds position frequency matrices
using an advanced Gibbs sampling algorithm implemented in external
\&\fIGibbs\fR program by Chip Lawrence. The algorithm can produce
multiple patterns from a single set of sequences.
.SS new
.IX Subsection "new"
.Vb 10
\& 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 \*(AqGibbs\*(Aq
\&            \-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
.Ve
.SS pattern
.IX Subsection "pattern"
.SS all_patterns
.IX Subsection "all_patterns"
.SS patternSet
.IX Subsection "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.