oracular (3) Bio::Matrix::PSM::InstanceSiteI.3pm.gz

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

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