NAME

       TFBS::Word - IUPAC DNA consensus word-based pattern class =head1 DESCRIPTION

       TFBS::Word is a base class consisting of universal constructor called by its subclasses
       (TFBS::Matrix::*), and word pattern manipulation methods that are independent of the word
       type. It is not meant to be instantiated itself.

FEEDBACK

       Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard

       Boris Lenhard <Boris.Lenhard@cgb.ki.se>

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       preceded with an underscore.

   new
        Title   : new
        Usage   : my $pwm = TFBS::Matrix::PWM->new(%args)
        Function: constructor for the TFBS::Matrix::PWM object
        Returns : a new TFBS::Matrix::PWM object
        Args    : # you must specify the -word argument:
                  -word,       # a strig consisting of letters in
                               # IUPAC degenerate DNA alphabet
                               # (any of ACGTSWKMPYBDHVN)

                  #######

                  -name,        # string, OPTIONAL
                  -ID,          # string, OPTIONAL
                  -class,       # string, OPTIONAL
                  -tags         # a hash reference reference, OPTIONAL

   search_seq
        Title   : search_seq
        Usage   : my $siteset = $pwm->search_seq(%args)
        Function: scans a nucleotide sequence with the pattern represented
                  by the PWM
        Returns : a TFBS::SiteSet object
        Args    : # you must specify either one of the following three:

                  -file,       # the name od a fasta file (single sequence)
                     #or
                  -seqobj      # a Bio::Seq object
                               # (more accurately, a Bio::PrimarySeqobject or a
                               #  subclass thereof)
                     #or
                  -seqstring # a string containing the sequence

                  -max_mismatches,  # number of allowed positions in the site that do
                                    # not match the consensus
                                            # OPTIONAL: default 0

   search_aln
        Title   : search_aln
        Usage   : my $site_pair_set = $pwm->search_aln(%args)
        Function: Scans a pairwise alignment of nucleotide sequences
                  with the pattern represented by the word: it reports only
                  those hits that are present in equivalent positions of both
                  sequences and exceed a specified threshold score in both, AND
                  are found in regions of the alignment above the specified
                  conservation cutoff value.
        Returns : a TFBS::SitePairSet object
        Args    : # you must specify either one of the following three:

                  -file,       # the name of the alignment file in Clustal
                                      format
                     #or
                  -alignobj      # a Bio::SimpleAlign object
                               # (more accurately, a Bio::PrimarySeqobject or a
                               #  subclass thereof)
                     #or
                  -alignstring # a multi-line string containing the alignment
                               # in clustal format
                  #############

                  -max_mismatches,  # number of allowed positions in the site that do
                                     # not match the consensus
                                             # OPTIONAL: default 0

                  -window,     # size of the sliding window (inn nucleotides)
                               # for calculating local conservation in the
                               # alignment
                               # OPTIONAL: default 50

                  -cutoff      # conservation cutoff (%) for including the
                               # region in the results of the pattern search
                               # OPTIONAL: default "70%"

   to_PWM
   validate_word
   length