Microarrays

For more information, please enter your email address.

The design of fixed or capture probes is a very simple process. Simply enter in the multiple target (template) sequences, go to the design tab, and for each target, select a fixed probe design. Visual OMP will then create a solution set that contains a single fixed probe for each target that has been checked for mishybridization against all other targets. In any single design, we can account for probe lengths, Tm, template secondary structure, hairpin folding, probe dimers, mishybridization and checks using BLAST. If you have a specific location within a gene which you would like to target due to a unique situation, Visual OMP can direct a probe to be designed at any specific range.

By enabling users to find quick solutions using lab tested default parameters or to completely customize parameters to a user’s unique technology, complete and accurate solutions can be solved for even the most complex situation. How can a software application solve such complex issues, such as a microarray? When necessary, all advanced parameters, such as specific cutoff values for mishybridization and target secondary structure are made fully accessible and customizable. In this way, we put the control back in the user’s hands, to be able to design probes for even the most unique situation.

How customizable are the parameters in Visual OMP? Visual OMP is able to easily solve any kind of request by turning verbal ideas into mathematical models. By setting minimum, maximum and optimal values as well as bonus and penalty weights for deviating from the optimum, it is possible to describe how to treat any single parameter. By combining relative parameters with each other, we can prioritize different aspects of a user’s need into a single cohesive design.

One of the truly distinctive qualities of Visual OMP, is that outside the design of probes, we have the ability to perform an in silico simulation to test our designs, see their interactions with each template and to visually assess all secondary structures of probes, templates or any combination thereof. The interaction between different fixed probes is automatically excluded and only the significant interactions between template strands and probes are reported. In fact, it is possible to input random template strands which can also be checked for interaction. For the curious investigators, it is also possible to view any possible template-template interactions.

When designing a microarray, we at DNA Software understand that it’s possible that a good portion of a chip may have already been designed and validated. A unique feature of the Visual OMP application is that we enable the ability to enter in previous designs into any experiment. That way, it is possible to build upon previous architecture so that Visual OMP can complement instead of replace existing work. Of course, it goes without saying that everything that Visual OMP designs, will be prescreened for interactions against your validated designs.

All simulations can also be corrected for surface effects and for density by using the 2 most recognized corrections for microarrays, those be SantaLucia and those be De Fotin. Keeping with the theme of customizability , it is also possible to enter in customized surface corrections for your unique microarray to get the most accurate simulation possible.