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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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Please direct usage questions or support issues to the mailing list:

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

AUTHOR - Stefan Kirov



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