| Bio::Matrix::PSM::InstanceSite(3pm) | User Contributed Perl Documentation | Bio::Matrix::PSM::InstanceSite(3pm) |
Bio::Matrix::PSM::InstanceSite - A PSM site occurrence
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
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.
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Bio::Matrix::PSM::InstanceSiteI implementation
Email skirov@utk.edu
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
Title : mid Usage : my $mid=$instance->mid; Function: Get/Set the motif id Throws : Example : Returns : scalar Args : scalar
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
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
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
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
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
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
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
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)
| 2018-10-27 | perl v5.26.2 |