---
name: "TFBS::Site"
section: "3pm"
platform: "linux"
package: "libtfbs-perl"
version: "0.7.1+ds-4+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/TFBS::Site"
---

# TFBS::Site(3pm)

a nucleotide sequence feature object representing (possibly putative) transcription factor binding site.

## 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 access 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.