Glossary

O

OMP - Oligonucleotide Modelling Platform

OMP is the underlying computational engine that contains all the parameters, algorithms and science behind Visual OMP.   It is a separate component from the Graphical User Interface (GUI) making it easily portable to different platforms and environments.   

OMP Blast Result (OBR)

This file contains the information generated while Blasting a sequence against a certain database.   

OMP Design File (ODF)

Contains all of the information necessary to design single or multiplex primers and/or probes given at least one starting target sequence.  Contains information about sequences, solution conditions, output constraints, weights, directory information, and possible amplicon information.  An ODF may contain a design for a probe, TaqMan Probe, RNA probe, fixed probe, allele probe pair, (forward or reverse) primer, primer pair.

OMP Experiment File (OEF)

A text file which contains all of the information necessary to run an experimental simulation.  Contains information about sequences, solution conditions, output constraints, weights, directory information, and Net TM.  

OMP Output File (OOF)

A text file which contains the results of a simulation.  Both the results summary and the crosshybridization are generated from the OOF.  

OMP Output File (OSF)

Contains the results of a design (ODF).  The OSF contains the designs and thermodynamics associated with single or multiplex probe and primer design.   

OMP Project File (OPF)

Contains information about which experiments (OEF's) the experiment contains.   

Optimal Structure

An optimal structure is considered the conformation into which a species is most likely to fold.  Optimal structures exist for monomers, homodimers and heterodimers, etc.   

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