TFBS::PatternGen::MEME(3) a pattern factory that uses the MEME program


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


TFBS::PatternGen::MEME builds position frequency matrices using an external program MEME written by Bailey and Elkan. For information and source code of MEME see


Please send bug reports and other comments to the author.

AUTHOR - Wynand Alkema

Wynand Alkema <[email protected]>


 Title   : new
 Usage   : my $patterngen = TFBS::PatternGen::YMF->new(%args);
 Function: the constructor for the TFBS::PatternGen::MEME object
 Returns : a TFBS::PatternGen::MEME 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 the 'meme' executable
                          #  OPTIONAL: default 'meme'
            -additional_params  # a string containing additional
                                #   command-line switches for the
                                #   meme program




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.