Frequently Asked Questions

Science Technology Q. Why was Visual OMPTM developed? Q. How does Visual OMPTM simulate nucleic acid hybridization? Q. What applications can Visual OMPTM simulate or analyze? Q. What factors affect hybridization? Q. How is secondary structure computed within the software? Q. What is the nearest-neighbor model? Why is this important? Q. Can Visual OMPTM determine structures that may appear but are likely to be less prevalent? If so, how can I study these structures. Q. Why is primer and probe modeling necessary? Q. Where did this science and database come from? Software Q. What is Visual OMPTM? Q. How does it work? Q. Does Visual OMPTM perform biochip/microarray design? Q. Does Visual OMPTM design probes and primers? Q. Does Visual OMPTM support flexible Input Formats, such as sequences in GenBank, Fasta? Q. Can I use the analysis tool kit to go back and look at past experiments? Q. What are the visualization capabilities? Can I manipulate the visualization? Q. What is the type of file formats utilized by Visual OMPTM? Q. How many users can utilize Visual OMPTM at once? Q. Do you have any case studies on the performance and predictions of the software? Q. What applications do you have case studies on? Product Specifications and General Information Q. How do I order Visual OMPTM? Q. Do you accept credit cards? Q. What are the system requirements for Visual OMPTM installation? Q. Is Visual OMPTM client/server? How do I share data with colleagues? Q. On what operating system/environment does Visual OMPTM best run? Q. Does Visual OMPTM work over the web? Q. How do I get more support for Visual OMPTM? Q. What time is it at DNA Software right now? Answers Science Technology Q. Why was Visual OMPTM developed? Visual OMPTM was built to provide a graphical interface for OMPTM (Oligonucleotide Modeling PlatformTM), originally the brainchild of the chief scientist and founder, Dr. John SantaLucia. Many people familiar with OMPTM were impressed by its predictive power but were disappointed by the lack of a user interface. And so, Visual OMPTM was born to let scientists harness the power of OMPTM through an easy to use graphical interface. Q. How does Visual OMPTM simulate nucleic acid hybridization? Visual OMPTM 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 OMPTM 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: Application Oligonucleotide function PCR: - single target PCR - multiplex PCR - RT-PCR - Q-PCR Primer Pairs / Probes Sequencing: - conventional - sequencing by hybridization Primers Probe microarrays Gene Expression Profiling Probe microarrays Molecular Diagnostics: - polymorphism detection - genetic disorder diagnosis - pathogen detection - paternity testing - criminal investigation Primer Pairs / Probes: - Molecular Beacons, - TaqMan, - Invader assay, - Scorpion probes Q. What factors affect hybridization? The major factors that affect nucleic acid hybridization are: Assay Temperature which affects the equilibrium constant, hence the amount of binding. Cation Concentration (K+, Na+, Mg++ etc. ) which affects the stability of one oligonucleotide binding to another. Buffer Additives/Consistencies such as denaturants or viscosity. Secondary Structure which affects any oligonucleotide and its ability to bind to another oligonucleotide or itself. 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 OMPTM 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 OMPTM determine structures that may appear but are likely to be less prevalent? If so, how can I study these structures. Yes. Visual OMPTM 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 OMPTM 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 OMPTM 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 OMPTM 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 OMPTM 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 OMPTM 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 OMPTM 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 OMPTM perform biochip/microarray design? This is a yes/no question. Currently it is not possible to input 30 or so genes and have Visual OMPTM output an ideal solution. We have found that most users have probes already designed and need Visual OMPTM to troubleshoot why arrays are not functioning as predicted. In this case, Visual OMPTM 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 OMPTM 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 OMPTM design probes and primers? Yes. Visual OMPTM 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 OMPTM is also able to design allele specific primers and probes even around single SNP sites. Whatever your needs, Visual OMPTM provides the complete answer for any probe and primer design. Q. Does Visual OMPTM support flexible Input Formats, such as sequences in GenBank, Fasta? Yes. Visual OMPTM 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 OMPTM 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 OMPTM 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 OMPTM? Visual OMPTM 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 OMPTM 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 OMPTM at once? Currently, Visual OMPTM is limited to individual computers. However, any number of users may use and access Visual OMPTM 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 OMPTM. 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 OMPTM 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 OMPTM 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 OMPTM 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 OMPTM? Orders are accepted by purchase order, on line, facsimile, telephone, and credit card. Orders can be sent to: DNA Software, Inc., Attn: Sales Department, 204 East Washington Street, Ann Arbor, MI 48104 Orders can be faxed to: +1 (734) 222-9087, Attn: Sales Department Orders can be placed by phone, by dialing +1 (734) 222-9080 Q. Do you accept credit cards? Yes, we accept credit cards. 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 OMPTM 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 OMPTM client/server? How do I share data with colleagues? Currently Visual OMPTM is designed for individual machines. Although experiments and simulations must be designed and performed on a machine with Visual OMPTM installed, data may be shared easily. Visual OMPTM 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 OMPTM best run? Visual OMPTM 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 OMPTM work over the web? Currently, Visual OMPTM is designed only for use on individual workstations. Q. How do I get more support for Visual OMPTM? Authorized users may contact DNA Software for detailed support. Hours: Monday – Friday between 9 AM – 6 PM Eastern Time Phone: +1 (734) 222-9092 E-mail: support@DNAsoftware.com Q. What time is it at DNA Software right now? Find out here.