Bio::Matrix::PSM::InstanceSite(3pm)			User Contributed Perl Documentation		       Bio::Matrix::PSM::InstanceSite(3pm)

NAME

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

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

   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)

perl v5.14.2							    2012-03-02				       Bio::Matrix::PSM::InstanceSite(3pm)