/ 
BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Matrix::PSM::InstanceSiteI

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