Glossary

S

Scorpion primer

An oligonucleotide that consists of a probe linked to a primer. The probe part of the scorpion is complimentary to the extension product of the primer and will bind to this after extension.

Secondary structure

The two-dimensional structure of a DNA- or RNA-sequence under the given solution conditions.  

Sequence End (Seq End)

The Sequence end is the terminal position of the nucleotide in which a subsequence is declared.  Therefore, in the sequences tab in Visual OMP, if a sequence has 4000 nucleotides, but you would only like to consider nucleotides 3000-3100, then the sequence end would be 3100.

Sequence Start (Seq Start)

The Sequence start is the beginning position of the nucleotide in which a subsequence is declared.  Therefore, in the sequences Tab in Visual OMP, if a sequence has 4000 nucleotides, but you would only like to consider nucleotides 3000-3100, then the sequence start would be 3000.

Simulation

Simulation is the process by which Visual OMP takes a given number of sequences, their respective concentrations, and known solution conditions and predicts their interactions, thermodynamics, concentrations and percent bound features.  Simulation differs from Design in that Design takes in sequence and solution information and returns solutions which include oligos such as primers or probes.

Species

A species is defined as a state in which one or more sequences may be hybridized.  In other words, a species may be a folded monomer, random coil monomer, homodimer, heterodimer, trimer etc...  

Suboptimal

A suboptimal or "suboptimal structure" is a structure for a species that is not the most likely to occur.  For example, in a experiment with only one 50 mer, after a simulation, OMP will show that the sequence will most likely fold into one conformation (Optimal) and possibly into less likely conformations (Suboptimal).  Any species may have any number of suboptimal structures.  If a suboptimal exists such that it has the same energies as the optimal, then each structure is equally likely to occur.

Suboptimal Minimum Distance

Suboptimal Minimum Distance is one of the tools a user may utilize to determine suboptimal structures.  The distance function is a measure of similarity.  It can be defined as the minimum number of insertions, deletions and substitutions required to convert structure A to structure B.  A valid input for this keyword enables the user to define the minimum difference between an optimal structure and the first suboptimal structure.

Suboptimal Energy Threshold

Suboptimal Energy Threshold is one of the tools a user may utilize to determine suboptimal structures.  Suboptimal Energy Threshold is the maximum energy in kcal/mol that the delta G of a suboptimal structure can be away from the optimal structure at the assay temperature.  If this threshold is set to 1 kcal/mol for example and the optimal structure for a target is -5.67 kcal/mol, then OMP will return all suboptimal structures between -5.67 and -4.67 kcal/mol.

Suboptimal Threshold (% of Optimal)

The Suboptimal Threshold descriptions calculate the amount of structures by percentage of the optimal structure that OMP should report to the user using traceback.  For example, if the suboptimal window for a monomer is set to 50% and the optimal (most likely structure) ∆G for the sequence is -5 kcal/mol, then OMP will return all structures with a ∆G between -2.5 and –5 kcal/mol.

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