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)