Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::Matrix::PSM::InstanceSite - A PSM site occurrence

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, -anchor=>'CHR7', -start=>35000921, -end=>35000926);

         #Last 2 arguments are passed to create a Bio::LocatableSeq object
         #Anchor shows the coordinates system for the Bio::LocatableSeq object

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://github.com/bioperl/bioperl-live/issues

   Description
       Bio::Matrix::PSM::InstanceSiteI implementation

AUTHOR - Stefan Kirov

       Email skirov@utk.edu

APPENDIX

   new
        Title   : new
        Usage   : my $isntance=Bio::Matrix::PSM::InstanceSite->new
                                (-seq=>'TATAAT', -id=>"TATAbox1",
                                 -accession_number='ENSG00000122304', -mid=>'TB1',
                                 -desc=>'TATA box, experimentally verified in PRM1 gene',
                                 -relpos=>-35, -anchor=>'CHR7', -start=>35000921, -end=>35000926, strand=>1)
        Function: Creates an InstanceSite object from memory.
        Throws  :
        Example :
        Returns : Bio::Matrix::PSM::InstanceSite object
        Args    : hash

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

   anchor
        Title   : anchor
        Usage   : my $anchor=$instance->anchor;
        Function: Get/Set the anchor which shows what coordinate system start/end use
        Throws  :
        Example :
        Returns : string
        Args    : string

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

   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  :
        Example :
        Returns : integer
        Args    : integer

   annotation
        Title   : annotation
        Usage   : $ann = $seq->annotation or $seq->annotation($annotation)
        Function: Gets or sets the annotation
        Returns : L<Bio::AnnotationCollectionI> object
        Args    : None or L<Bio::AnnotationCollectionI> object

       See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information

   species
        Title   : species
        Usage   : $species = $seq->species() or $seq->species($species)
        Function: Gets or sets the species
        Returns : L<Bio::Species> object
        Args    : None or L<Bio::Species> object

       See Bio::Species for more information

   frame
        Title   : frame
        Usage   : my $frane=$instance->frame;
        Function: Get/Set the frame of a DNA instance with respect to a protein motif used.
                   Returns undef if the motif was not protein or the DB is protein.
        Throws  :
        Example :
        Returns : integer
        Args    : integer (0, 1, 2)