Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a PSM
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);
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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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