---
name: "Bio::Matrix::PSM::InstanceSite"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Matrix::PSM::InstanceSite"
---

# Bio::Matrix::PSM::InstanceSite(3pm)

A PSM site occurrence

## NAME

Bio::Matrix::PSM::InstanceSite - A PSM site occurrence

## SYNOPSIS

```
  use Bio::Matrix::PSM::InstanceSite;
  #You can get an InstanceSite object either from a file:
  my ($instances,$matrix)=$SomePSMFile->parse_next;
  #or from memory
  my %params=(seq=>'TATAAT',
    id=>"TATAbox1", accession=>'ENSG00000122304', mid=>'TB1',
    desc=>'TATA box, experimentally verified in PRM1 gene',
    -relpos=>-35, -anchor=>'CHR7', -start=>35000921, -end=>35000926);
  #Last 2 arguments are passed to create a Bio::LocatableSeq object
  #Anchor shows the coordinates system for the Bio::LocatableSeq object
```

## DESCRIPTION

Abstract interface to PSM site occurrence (PSM sequence match). InstanceSite objects may be used to describe a PSM (See Bio::Matrix::PSM::SiteMatrix) sequence matches.  The usual characteristic of such a match is sequence coordinates, score, sequence and sequence (gene) identifier- accession number or other id.

This object inherits from Bio::LocatableSeq (which defines the real sequence) and might hold a SiteMatrix object, used to detect the CRE (cis-regulatory element), or created from this CRE.

While the documentation states that the motif id and gene id (accession) combination should be unique, this is not entirely true- there might be more than one occurrence of the same cis-regulatory element in the upstream region of the same gene.  Therefore relpos would be the third element to create a really unique combination.

## FEEDBACK

### Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists.  Your participation is much appreciated.

```
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
```

### Support

Please direct usage questions or support issues to the mailing list:

*bioperl-l@bioperl.org*

rather than to the module maintainer directly. Many experienced and  reponsive experts will be able look at the problem and quickly  address it. Please include a thorough description of the problem  with code and data examples if at all possible.

### Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the web:

```
  https://github.com/bioperl/bioperl-live/issues
```

### Description

Bio::Matrix::PSM::InstanceSiteI implementation

## AUTHOR - Stefan Kirov

Email skirov@utk.edu

## APPENDIX

### new

```
 Title   : new
 Usage   : my $isntance=Bio::Matrix::PSM::InstanceSite->new
                         (-seq=>'TATAAT', -id=>"TATAbox1",
                          -accession_number='ENSG00000122304', -mid=>'TB1',
                          -desc=>'TATA box, experimentally verified in PRM1 gene',
                          -relpos=>-35, -anchor=>'CHR7', -start=>35000921, -end=>35000926, strand=>1)
 Function: Creates an InstanceSite object from memory.
 Throws  :
 Example :
 Returns : Bio::Matrix::PSM::InstanceSite object
 Args    : hash
```

### mid

```
 Title   : mid
 Usage   : my $mid=$instance->mid;
 Function: Get/Set the motif id
 Throws  :
 Example :
 Returns : scalar
 Args    : scalar
```

### score

```
 Title   : score
 Usage   : my $score=$instance->score;
 Function: Get/Set the score (mismatches) between the instance and the attached (or
            initial) PSM
 Throws  :
 Example :
 Returns : real number
 Args    : real number
```

### anchor

```
 Title   : anchor
 Usage   : my $anchor=$instance->anchor;
 Function: Get/Set the anchor which shows what coordinate system start/end use
 Throws  :
 Example :
 Returns : string
 Args    : string
```

### start

```
 Title   : start
 Usage   : my $start=$instance->start;
 Function: Get/Set the position of the instance on the sequence used
 Throws  :
 Example :
 Returns : integer
 Args    : integer
```

### minstance

```
 Title   : minstance
 Usage   : my $minstance=$misntance->score;
 Function: Get/Set the unique identifier- sequence id/motif id, for example PRM1_TATAbox.
          Not necessarily human readable.
 Throws  :
 Example :
 Returns : string
 Args    : string
```

### relpos

```
 Title   : relpos
 Usage   : my $seqpos=$instance->relpos;
 Function: Get/Set the relative position of the instance with respect to the transcription start
            site (if known). Can and usually is negative.
 Throws  :
 Example :
 Returns : integer
 Args    : integer
```

### annotation

```
 Title   : annotation
 Usage   : $ann = $seq->annotation or $seq->annotation($annotation)
 Function: Gets or sets the annotation
 Returns : L<Bio::AnnotationCollectionI> object
 Args    : None or L<Bio::AnnotationCollectionI> object
```

See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information

### species

```
 Title   : species
 Usage   : $species = $seq->species() or $seq->species($species)
 Function: Gets or sets the species
 Returns : L<Bio::Species> object
 Args    : None or L<Bio::Species> object
```

See Bio::Species for more information

### frame

```
 Title   : frame
 Usage   : my $frane=$instance->frame;
 Function: Get/Set the frame of a DNA instance with respect to a protein motif used.
            Returns undef if the motif was not protein or the DB is protein.
 Throws  :
 Example :
 Returns : integer
 Args    : integer (0, 1, 2)
```