my $patterngen =
-binary => 'meme'
my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
DESCRIPTIONTFBS::PatternGen::MEME builds position frequency matrices using an external program MEME written by Bailey and Elkan. For information and source code of MEME see
FEEDBACKPlease send bug reports and other comments to the author.
AUTHOR - Wynand AlkemaWynand 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
patternSetThe 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.