TFBS::PatternGen::MEME(3pm)

NAME

TFBS::PatternGen::MEME - a pattern factory that uses the MEME program

SYNOPSIS

my $patterngen =
        TFBS::PatternGen::MEME->new(-seq_file=>'sequences.fa',
                                        -binary => 'meme'


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

DESCRIPTION

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

http://www.sdsc.edu/MEME

FEEDBACK

Please send bug reports and other comments to the author.

AUTHOR - Wynand Alkema

Wynand Alkema <Wynand.Alkema@cgb.ki.se>
new: Title : new
Usage : my $pattrengen = TFBS::PatternGen::MEME->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
pattern
all_patterns
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.

docs.sk