Provided by: libbio-perl-perl_1.7.2-2_all bug


       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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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