Bio::Matrix::PSM
InstanceSiteI
Summary
Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a PSM
Package variables
No package variables defined.
Inherit
Synopsis
use Bio::Matrix::PSM::InstanceSite;
#Y ou 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);
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.
Methods
Methods description
Title : mid
Usage : my $mid=$instance->mid;
Function: Get/Set the motif id
Throws :
Returns : scalar
Args : scalar |
Title : score
Usage : my $score=$instance->score;
Function: Get/Set the score (mismatches) between the instance and the attached (or
initial) PSM
Throws :
Returns : real number
Args : real number |
Title : start
Usage : my $start=$instance->start;
Function: Get/Set the position of the instance on the sequence used
Throws :
Returns : integer
Args : integer |
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 :
Returns : integer
Args : integer |
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 :
Returns : string
Args : string |
Methods code
sub mid
{ my $self = shift;
$self->throw_not_implemented();} | sub score
{ my $self = shift;
$self->throw_not_implemented();} | sub start
{ my $self = shift;
$self->throw_not_implemented();} | sub relpos
{ my $self = shift;
$self->throw_not_implemented();} | sub minstance
{ my $self = shift;
$self->throw_not_implemented();} | General documentation
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