/ 
BioPerl-1.007000_004
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Matrix::PSM::InstanceSite

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://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)