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.\" ========================================================================
.\"
.IX Title "TFBS::PatternGen::Elph 3"
.TH TFBS::PatternGen::Elph 3 "2005-01-04" "perl v5.12.4" "User Contributed Perl Documentation"
.\" For nroff, turn off justification. Always turn off hyphenation; it makes
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.SH "NAME"
TFBS::PatternGen::Elph \- a pattern factory that uses the Elph program
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 5
\& my $patterngen =
\& TFBS::PatternGen::Elph\->new(\-seq_file=>\*(Aqsequences.fa\*(Aq,
\& \-binary => \*(Aq/Elph/elph\*(Aq
\& \-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.
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