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

       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_PWMvalidate_wordlength
perl v5.40.0                                       2024-10-20                         TFBS::Word::Consensus(3pm)

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

       Please send bug reports and other comments to the author.

       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.