NAME¶
Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a
PSM
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.
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
AUTHOR - Stefan Kirov¶
Email skirov@utk.edu
SEE ALSO¶
Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::Psm, Bio::Matrix::PSM::IO
APPENDIX¶
mid¶
Title : mid
Usage : my $mid=$instance->mid;
Function: Get/Set the motif id
Throws :
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 :
Returns : real number
Args : real number
start¶
Title : start
Usage : my $start=$instance->start;
Function: Get/Set the position of the instance on the sequence used
Throws :
Returns : integer
Args : integer
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 :
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 :
Returns : string
Args : string