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Bio::Matrix::PSM::InstanceSiteI.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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