NAME

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

SYNOPSIS

         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);

DESCRIPTION

       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.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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

       bioperl-l@bioperl.org

       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:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Stefan Kirov

       Email skirov@utk.edu

SEE ALSO

       Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::Psm, Bio::Matrix::PSM::IO

APPENDIX

   mid
        Title   : mid
        Usage   : my $mid=$instance->mid;
        Function: Get/Set the motif id
        Throws  :
        Returns : scalar
        Args    : scalar

   score
        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

   start
        Title   : start
        Usage   : my $start=$instance->start;
        Function: Get/Set the position of the instance on the sequence used
        Throws  :
        Returns : integer
        Args    : integer

   relpos
        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

   minstance
        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