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.IX Title "TFBS::PatternGen::SimplePFM 3pm"
.TH TFBS::PatternGen::SimplePFM 3pm 2024-03-13 "perl v5.38.2" "User Contributed Perl Documentation"
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.SH NAME
TFBS::PatternGen::SimplePFM \- a simple position frequency matrix factory
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 6
\&    my @sequences = qw( AAGCCT AGGCAT AAGCCT
\&                        AAGCCT AGGCAT AGGCCT
\&                        AGGCAT AGGTTT AGGCAT
\&                        AGGCCT AGGCCT );
\&    my $patterngen =
\&            TFBS::PatternGen::SimplePFM\->new(\-seq_list=>\e@sequences);
\&  
\&    my $pfm = $patterngen\->pattern(); # $pfm is now a TFBS::Matrix::PFM object
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
TFBS::PatternGen::SimplePFM generates a position frequency matrix from a set
of nucleotide sequences of equal length, The sequences can be passed either
as strings, as Bio::Seq objects or as a fasta file.
.PP
This pattern generator always creates only one pattern from a given set
of sequences.
.SS new
.IX Subsection "new"
.Vb 10
\& Title   : new
\& Usage   : my $db = TFBS::PatternGen::SimplePFM\->new(%args);
\& Function: the constructor for the TFBS::PatternGen::SimplePFM
\&            object
\& Returns : a TFBS::PatternGen::SimplePFM obkect
\& Args    : This method takes named arguments;
\&            you must specify one of the following
\&            \-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
.Ve
.SS pattern
.IX Subsection "pattern"
.SS all_patterns
.IX Subsection "all_patterns"
.SS patternSet
.IX Subsection "patternSet"
The three above methods are used fro the retrieval of patterns,
and are common to all TFBS::PatternGen::* classes. Please
see TFBS::PatternGen for details.