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.\" ========================================================================
.\"
.IX Title "TFBS::Word::Consensus 3pm"
.TH TFBS::Word::Consensus 3pm "2008-01-24" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
TFBS::Word \- IUPAC DNA consensus word\-based pattern class
=head1 DESCRIPTION
.PP
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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
Please send bug reports and other comments to the author.
.SH "AUTHOR \- Boris Lenhard"
.IX Header "AUTHOR - Boris Lenhard"
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
.SS "new"
.IX Subsection "new"
.Vb 8
\& 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
.Ve
.SS "search_seq"
.IX Subsection "search_seq"
.Vb 6
\& 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
.Ve
.SS "search_aln"
.IX Subsection "search_aln"
.Vb 10
\& 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%"
.Ve
.SS "to_PWM"
.IX Subsection "to_PWM"
.SS "validate_word"
.IX Subsection "validate_word"
.SS "length"
.IX Subsection "length"