Frequently Asked Questions

Science Technology

Software

Product Specifications and General Information

Answers

Science Technology

Q. Why was Visual OMP developed?

Visual OMP was built to provide a graphical interface for OMP (Oligonucleotide Modeling Platform), originally the brainchild of the chief scientist and founder, Dr. John SantaLucia. Many people familiar with OMP were impressed by its predictive power but were disappointed by the lack of a user interface. And so, Visual OMP was born to let scientists harness the power of OMP through an easy to use graphical interface.

Q. How does Visual OMP simulate nucleic acid hybridization?

Visual OMP 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 Visual OMP 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?

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

Yes. Visual OMP 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 Visual OMP 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.

Example: The analysis of a 40 mer oligonucleotide created by Visual OMP shows three significant structures:

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 Visual OMP 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 Visual OMP?

Visual OMP has been designed to be the first and last reference that scientists turn to when developing, analyzing or simulating a nucleic acid based experiment. 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?

Visual OMP 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 Visual OMP 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 Visual OMP perform biochip/microarray design?

This is a yes/no question. Currently it is not possible to input 30 or so genes and have Visual OMP output an ideal solution. We have found that most users have probes already designed and need Visual OMP to troubleshoot why arrays are not functioning as predicted. In this case, Visual OMP is able to take all probes and simulate their interaction with all targets to determine where there is significant cross-hybridization or mishybridization. In fact, Visual OMP will also show if the secondary structure of either targets or probes pose significant problems. Using the cross-hybridization grid, a user may visually inspect all interactions between oligos in seconds, and determine the problem probes and targets. Following these procedures will help to design a tighter and more accurate array.

Q. Does Visual OMP design probes and primers?

Yes. Visual OMP is not only able to design primers and probes, but it can design multiple primers and probes at the same time and check for interactions between potential targets and oligos. In one quick simulation, it is possible to design a complete multiplex solution for your assay. Visual OMP is also able to design allele specific primers and probes even around single SNP sites. Whatever your needs, Visual OMP provides the complete answer for any probe and primer design.

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

Yes. Visual OMP allows direct import, or cutting and pasting into the sequences tab. That way, a user can open up a Fasta file or Genbank file directly or cut and paste sequences directly into an experiment.

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

Yes. In fact one of the strengths of Visual OMP is that it will allow users to change experimental settings, rerun experiments and compare them to previous trials, all with the click of a few buttons.

Q. What are the visualization capabilities? Can I manipulate the visualization?

Visual OMP allows users to visualize experimental results in 3 major ways: Secondary Structure Analysis, Numerical Analysis, and Cross-hybridization Analysis. Secondary Structure Analysis may be manipulated to publication quality and easily exported in any major graphic format. Numerical Analysis may also be manipulated although graphical tools remain limited. An easy export tool will allow a user to recreate the numerical analysis in Excel when manipulation might be more familiar. Lastly, the cross-hybridization grid, which allows users to visualize all heterodimer relations, may be "filtered" so that a user may customize the importance of interactions with colors.

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

Visual OMP 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, Visual OMP 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 Visual OMP at once?

Currently, Visual OMP is limited to individual computers. However, any number of users may use and access Visual OMP 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 Visual OMP. 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 Visual OMP 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 Visual OMP 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, Visual OMP has had contact in some form or another with most major nucleic based techniques. Product Specifications and General Information

Q. How do I order Visual OMP?

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 (734) 222-9087

Orders can be placed by phone, by dialing +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 Visual OMP installation?

A minimum P III 700 MHz with 128 MB of RAM, Windows 98/ 2000 / XP (With Service Pack) , 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 Visual OMP client/server? How do I share data with colleagues?

Currently Visual OMP is designed for individual machines. Although experiments and simulations must be designed and performed on a machine with Visual OMP installed, data may be shared easily. Visual OMP contains many shortcuts and concepts integrated to allow users to seamlessly move from data or graphics to or from common Microsoft products such as Word, Excel, or Powerpoint.

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

Visual OMP is currently optimized for Windows XP and Windows 2000 operating systems. Also, for full functionality, it is suggested that either Excel XP or Excel 2000 be installed. Users wishing to run experiments on a Linux platform may contact sales at: sales@dna-software.com

Q. Does Visual OMP work over the web?

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

Q. How do I get more support for Visual OMP?

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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