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
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Support
Please direct usage questions or support issues to the mailing list:
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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)