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TFBS::Site(3pm) 					User Contributed Perl Documentation					   TFBS::Site(3pm)

NAME

       TFBS::Site - a nucleotide sequence feature object representing (possibly putative) transcription factor binding site.

SYNOPSIS

	   # manual creation of site object;
	   # for details, see documentation of Bio::SeqFeature::Generic;

	   my $site = TFBS::Site
			 (-start => $start_pos,     # integer
			  -end	 => $end_pos,	    # integer
			  -score => $score,	    # float
			  -source => "TFBS",	    # string
			  -primary => "TF binding site",  # primary tag
			  -strand => $strand,	    # -1, 0 or 1
			  -seqobj => $seqobj,	    # a Bio::Seq object whose sequence
						    #		 contains the site
			  -pattern => $pattern_obj  # usu. TFBS::Matrix:PWM obj.
			  -);

	   # Searching sequence with a pattern (PWM) and retrieving individual sites:
	   #
	   #   The following objects should be defined for this example:
	   #	   $pwm    -   a TFBS::Matrix::PWM object
	   #	   $seqobj -   a Bio::Seq object
	   #   Consult the documentation for the above modules if you do not know
	   #   how to create them.

	   #   Scanning sequence with $pwm returns a TFBS::SiteSet object:

	   my $site_set = $pwm->search_seq(-seqobj => $seqobj,
					   -threshold => "80%");

	   #   To retrieve individual sites from $site_set, create an iterator obj:

	   my $site_iterator = $site_set->Iterator(-sort_by => "score");

	   while (my $site = $site_iterator->next())  {
	       # do something with $site
	   }

DESCRIPTION

       TFBS::Site object holds data for a (possibly predicted) transcription factor binding site on a nucleotide sequence (start, end, strand,
       score, tags, as well as references to the corresponding sequence and pattern objects). TFBS::Site is a subclass of Bio::SeqFeature::Generic
       and has acces to all of its method. Additionally, it contains the pattern() method, an accessor for pattern object associated with the site
       object.

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.

       TFBS::Site is a class that extends Bio::SeqFeature::Generic. Please consult Bio::SeqFeature::Generic documentation for other available
       methods.

   new
	Title	: new
	Usage	: my $site = TFBS::Site->new(%args)
	Function: constructor for the TFBS::Site object
	Returns : TFBS::Site object
	Args	: -start,	# integer
		  -end, 	# integer
		  -strand,	# -1, 0 or 1
		  -score,	# float
		  -source,	# string (method used to detect it)
		  -primary,	# string (primary tag)
		  -seqobj,	# a Bio::Seq object
		  -pattern	# a pattern object, usu. TFBS::Matrix::PWM

   pattern
	Title	: pattern
	Usage	: my $pattern = $site->pattern();  # gets the pattern
		  $site->pattern($pwm); 	   # sets the pattern to $pwm
	Function: gets/sets the pattern object associated with the site
	Returns : pattern object, here TFBS::Matrix::PWM object
	Args	: pattern object (optional, for setting the pattern only)

   rel_score
	Title	: rel_score
	Usage	: my $percent_score = $site->rel_score() * 100;  # gets the pattern
	Function: gets relative score (between 0.0 to 1.0) with respect of the score
		  range of the associated pattern (matrix)
	Returns : floating point number between 0 and 1,
		  or undef if pattern not defined
	Args	: none

   GFF
	Title	: GFF
	Usage	: print $site->GFF();
		: print $site->GFF($gff_formatter)
	Function: returns a "standard" GFF string - the "generic" gff_string
		  method is left untouched for possible customizations
	Returns : a string (NOT newline terminated! )
	Args	: a $gff_formatter function reference (optional)

   location
   start
   end
   length
   score
   frame
   sub_SeqFeature
   add_sub_SeqFeature
   flush_sub_SeqFeature
   primary_tag
   source_tag
   has_tag
   add_tag_value
   each_tag_value
   all_tags
   remove_tag
   attach_seq
   seq
   entire_seq
   seq_id
   annotation
   gff_format
   gff_string
       The above methods are inherited from Bio::SeqFeature::Generic.  Please see Bio::SeqFeature::Generic for details on their usage.

perl v5.14.2							    2008-01-24							   TFBS::Site(3pm)