Bio::Matrix::PSM::InstanceSite - A PSM site occurance 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); 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.

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Description
Bio::Matrix::PSM::InstanceSiteI implementation Email skirov@utk.edu

new
Title : new Usage : my $isntance=new Bio::Matrix::PSM::InstanceSite (-seq=>'TATAAT', -id=>"TATAbox1", -accession_number='ENSG00000122304', -mid=>'TB1', -desc=>'TATA box, experimentally verified in PRM1 gene', -relpos=>-35) 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

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