Bio::Matrix::PSM InstanceSiteI
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Summary
Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a PSM
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
  use Bio::Matrix::PSM::InstanceSite;
#Y ou 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);
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.
Methods
midDescriptionCode
scoreDescriptionCode
startDescriptionCode
relposDescriptionCode
minstanceDescriptionCode
Methods description
midcode    nextTop
 Title   : mid
Usage : my $mid=$instance->mid;
Function: Get/Set the motif id
Throws :
Returns : scalar
Args : scalar
scorecodeprevnextTop
 Title   : score
Usage : my $score=$instance->score;
Function: Get/Set the score (mismatches) between the instance and the attached (or
initial) PSM
Throws :
Returns : real number
Args : real number
startcodeprevnextTop
 Title   : start
Usage : my $start=$instance->start;
Function: Get/Set the position of the instance on the sequence used
Throws :
Returns : integer
Args : integer
relposcodeprevnextTop
 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 :
Returns : integer
Args : integer
minstancecodeprevnextTop
 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 :
Returns : string
Args : string
Methods code
middescriptionprevnextTop
sub mid {
    my $self = shift;
    $self->throw_not_implemented();
}
scoredescriptionprevnextTop
sub score {
    my $self = shift;
    $self->throw_not_implemented();
}
startdescriptionprevnextTop
sub start {
    my $self = shift;
    $self->throw_not_implemented();
}
relposdescriptionprevnextTop
sub relpos {
    my $self = shift;
    $self->throw_not_implemented();
}
minstancedescriptionprevnextTop
sub minstance {
    my $self = shift;
    $self->throw_not_implemented();
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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/
AUTHOR - Stefan KirovTop
Email skirov@utk.edu
SEE ALSOTop
Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::Psm, Bio::Matrix::PSM::IO
APPENDIXTop