Bio::Matrix::PSM::InstanceSite

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

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Description

Bio::Matrix::PSM::InstanceSiteI implementation

AUTHOR - Stefan Kirov

Email [email protected]

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)