Bio::Matrix::PSM::InstUserSContributed Perl Bio::Matrix::PSM::InstanceSiteI(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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
perl v5.14.12011-07-22Bio::Matrix::PSM::InstanceSiteI(3)
