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SF.net: Site Status Page released!
07-21-2008
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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)