NAME

       TFBS::PatternGen::AnnSpec - a pattern factory that uses the AnnSpec program (version 2.1)

SYNOPSIS

           my $patterngen =
                   TFBS::PatternGen::AnnSpec->new(-seq_file=>'sequences.fa',
                                                   -binary => 'ann-spec '

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

DESCRIPTION

       TFBS::PatternGen::AnnSpec builds position frequency matrices using an external program
       AnnSpec (Workman, C. and Stormo, G.D. (2000) ANN-Spec: A method for discovering
       transcription factor binding sites with improved specificity. Proc. Pacific Symposium on
       Biocomputing 2000).

FEEDBACK

       Please send bug reports and other comments to the author.

AUTHOR - Wynand Alkema

       Wynand Alkema <Wynand.Alkema@cgb.ki.se<gt>

   new
        Title   : new
        Usage   : my $pattrengen = TFBS::PatternGen::AnnSpec->new(%args);
        Function: the constructor for the TFBS::PatternGen::AnnSpec object
        Returns : a TFBS::PatternGen::AnnSpec 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 'ann-spec'
                   -additional_params  # a string containing additional
                                       #   command-line switches for the
                                       #   ann-spec 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.