| Bio::Matrix::PSM::InstanceSiteI(3pm) | User Contributed Perl Documentation | Bio::Matrix::PSM::InstanceSiteI(3pm) |
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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Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::Psm, Bio::Matrix::PSM::IO
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
| 2021-08-15 | perl v5.32.1 |