OMP Developer Edition Frequently Asked Questions

Science Technology

Software

Product Specifications and General Information

Answers

Science Technology

Q. Why was OMP Developer Edition developed?

OMP Developer Edition was built to provide customizable, highthroughput capabilities to OMP (Oligonucleotide Modeling Platform), originally the brainchild of the chief scientist and founder, Dr. John SantaLucia. Those who are familar with OMP or the related graphical interface Visual OMP are probably already aware of the powerful predictive capabilities. OMP Developer Edition enables researchers the ability to develop around this engine, to apply the power of simulation to their own technology, and drive it to true highthroughput analysis.

Q. How does OMP Developer Edition simulate nucleic acid hybridization?

OMP Developer Edition uses the industry's most complete database of empirical parameters, combined with theoretical models and advanced computer algorithms to establish a "nearest neighbor model." The model is able to determine the thermodynamics of a multi-state equilibrium given assay experimental conditions and powerful enough to determine secondary structure motifs and suboptimal structures.

Q. What applications can OMP Developer Edition simulate or analyze?

The engine and user interface has been specifically designed to handle an extensive array of applications. Some of the more common applications include:

Q. What factors affect hybridization?

The major factors that affect nucleic acid hybridization are:

1. Assay Temperature which affects the equilibrium constant, hence the amount of binding.
2. Cation Concentration (K+, Na+, Mg++ etc. ) which affects the stability of one oligonucleotide binding to another.
3. Buffer Additives/Consistencies such as denaturants or viscosity.
4. Secondary Structure which affects any oligonucleotide and its ability to bind to another oligonucleotide or itself.
5. Synthetic nucleotide modification, such as Cy3 or Cy5 have the ability to increase or decrease binding.

Q. How is secondary structure computed within the software?

OMP Developer Edition uses a dynamic programming algorithm to calculate the energy of all possible structures by using our thermodynamic database. The optimal and nearby suboptimal structures are predicted to be most populated at equilibrium.

Q. What is the nearest-neighbor model? Why is this important?

The nearest-neighbor model uses empirical data to determine a set of "parameters" for all possible combinations of base pairs. By giving each base-pair a mathematical value, it is possible to quickly and accurately calculate the thermodynamics of any hybridization. The nearest neighbor model also accounts for initiation, symmetry, mismatches, dangling ends, internal loops, and bulges. An example shows how the NN model would be used to calculate the dG of a simple homodimer.

Q. Can OMP Developer Edition determine structures that may appear but are likely to be less prevalent? If so, how can I study these structures.

Yes. OMP Developer Edition has the ability to determine the presence of "suboptimal" structures. A suboptimal structure is defined as a structure of a sequence that is less energetically favorable than the structure that is most likely to appear. A OMP Developer Edition user may study these structures by looking at thermodynamics of the suboptimals or through a more user-friendly manner: Secondary structure display. Using secondary structure display, a user may look at the optimal and cycle through all pertinent suboptimal structures with the click of a button.

Q. Why is primer and probe modeling necessary?

Poor primer design is the one major cause of all failures in single and multiplex PCR. Similarly, poor probe design is the major cause of failure in many diagnostic assays such as those involving molecular beacons or scorpions. Primers and probes may fail for many different reasons, among them: mishybridization, significant internal secondary structure or homodimerization. Since these causes may lead to failure and/or false positives, proper primer or probe design becomes a necessary first step to many simple and most complex assays.

Q. Where did this science and database come from?

The underlying algorithms and database from which OMP Developer Edition draws its power is the culmination of many years of work from the John Santa Lucia laboratory. Many more parameters have been derived in house and from collaborations with other companies. At this point, the database is so complete, that accuracy for DNA duplex melting temperatures is on average 2ºC away from experimental results. Even so, DNA software continues to add more parameters to make our predictions even more precise.

Software

Q. What is OMP Developer Edition?

OMP Developer Edition has been designed to be the first and last reference that scientists turn to when developing, analyzing or simulating a nucleic acid based experiment. OMP Developer Edition is a fully customizable engine with the ability to perform high throught analysis on hundreds of thousands of sequences. It is robust enough to handle the most complex simulations, yet discreet enough to detect a single base pair mismatch.

Q. How does it work?

OMP Developer Edition works by simulating experiments and determining the structure, behavior and effectiveness of oligonucleotides in a multi-state equilibrium. In other words, it simulates performing a "wet" experiment without using a laboratory. Using OMP Developer Edition will save scientists from using trial and error methods of determining the shortfalls of experiments. The end result? Quicker assay development and analysis resulting in the most accurate and precise answers.

Q. Does OMP Developer Edition design probes and primers?

Yes. OMP Developer Edition can design probes and primer, even multiplex them at the same time. Probe and Primer design using OMP Deveper Edition can also be tailored to factor in Tms, lengths, binding affinites, homodimers, secondary structure, crosshybridizations with other probes or primers, mishybridizations against other targets among other considerations.

Q. Does OMP Developer Edition support flexible Input Formats, such as sequences in GenBank, Fasta?

No. OMP Developer Edition uses only OMP Experiment Files (OEF) and OMP Design Files (ODF) as legal inputs. All Genbank and Fasta formats must first be converted one of these two file formats before an experiment is run.

Q. Can I use the analysis tool kit to go back and look at past experiments?

Yes. In fact one of the strengths of OMP Developer Edition is that it will allow users to change experimental settings, rerun experiments and compare them to previous trials.

Q. What are the visualization capabilities?

OMP Developer Edition does not use a graphical interface. Secondary structures of species is available in text form and can be queried for useful information, or outputted to a custom user designed application for visualization.

Q. What is the type of file formats utilized by OMP Developer Edition?

OMP Developer Edition necessarily uses unique file formats for almost everything. Conventional file formats such as Fasta and Genbank have not been robustly designed to accept the complexity of information that is needed to simulate an experiment. However, OMP Developer Edition does fully accept Fasta and Genbank files as a starting point to make import easier for scientist familiar with these formats.

Q. How many users can utilize OMP Developer Edition at once?

Currently, OMP Developer Edition is limited to individual computers. However, any number of users may use and access OMP Developer Edition on any one workstation.

Q. Do you have any case studies on the performance and predictions of the software?

There are two main methods that DNA Software uses to validation the performance of OMP Developer Edition. Firstly, an in-house laboratory is able to produce and confirm any two state melting temperature of natural or modified oligonucleotides. Experimental melts for 2 state DNA melts are on average +/- 0.2 degrees away from OMP Developer Edition predictions. Secondly, DNA Software maintains dedicated servers to constantly run random sequences to determine anomalies. Since DNA Software's inception, there have been upwards of 100 million experiments run.

Q. What applications do you have case studies on?

The engine that drives OMP Developer Edition has successfully been used commercially to do wide-ranging applications such as microarray, multiplex PCR and microfluidics analysis as well as molecular beacon and scorpion design. In fact, OMP Developer Edition has had contact in some form or another with most major nucleic based techniques.

Product Specifications and General Information

Q. How do I order OMP Developer Edition?

Orders are accepted by purchase order, on line, facsimile, telephone, and credit card.

Orders can be sent to:
Attn: Sales Order Fulfillment
DNA Software, Inc.
204 E. Washington Ave.
Ann Arbor, MI 48104

Orders can be faxed to:
Attn: Sales Order Fulfillment +1 (734) 222-9087

Orders can be placed by phone, +1 (734)222-9080

Q. Do you accept credit cards? How do I know the transaction is safe?

Yes, we accept credit cards through PayPal, which utilizes the world's most advanced proprietary fraud prevention systems. For your protection, please do not send us your credit card number. Instead, contact us to arrange the transaction.

Q. What are the system requirements for OMP Developer Edition installation?

A minimum P III 700 MHz with 128 MB of RAM, Windows 2000 / XP (With Service Pack), Linux, 32-bit True Color Setting (Display Properties), screen resolution of at least 800 x 640. A user must administrator rights for the current login account.

Q. Is OMP Developer Edition client/server? How do I share data with colleagues?

Currently OMP Developer Edition is designed for individual machines. Although experiments and simulations must be designed and performed on a machine with OMP Developer Edition installed, data may be shared easily.

Q. On what operating system/environment does OMP Developer Edition best run?

OMP Developer Edition is currently optimized for Windows XP , Windows 2000 and Linux operating systems.

Q. Does OMP Developer Edition work over the web?

Currently, OMP Developer Edition is designed only for use on individual workstations.

Q. How do I get more support for OMP Developer Edition?

Authorized users may contact DNA software for detailed support.
Hours: Monday - Friday between 9 AM - 9 PM Eastern Time
Phone: +1 (734) 222-9092
E-mail: support@DNAsoftware.com

Q. What time is it at DNA Software right now?

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