NAME

       TFBS::PatternGen::SimplePFM - a simple position frequency matrix factory

SYNOPSIS

           my @sequences = qw( AAGCCT AGGCAT AAGCCT
                               AAGCCT AGGCAT AGGCCT
                               AGGCAT AGGTTT AGGCAT
                               AGGCCT AGGCCT );
           my $patterngen =
                   TFBS::PatternGen::SimplePFM->new(-seq_list=>\@sequences);

           my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object

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.

       This pattern generator always creates only one pattern from a given set of sequences.

   new
        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

   pattern
   all_patterns
   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.