Bio::Matrix::PSM::InstanceSite 1.4 review

Bio::Matrix::PSM::InstanceSite is a PSM site occurance. SYNOPSIS use Bio::Matrix::PSM::InstanceSite; #You can get an Ins

License: Perl Artistic License File size: 4788K Developer: Stefan Kirov

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Bio::Matrix::PSM::InstanceSite is a PSM site occurance.

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);

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.

Requirements:
Perl