VISUAL OMP

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VISUAL OMP

Postby smith » Wed Jul 27, 2011 3:06 pm

I want to buy Visual OMP. If anyone could please inform me about the list price and the academic price it would be a real help.
I also want to know about the licensing policy of the product .... Please help
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Re: VISUAL OMP

Postby stev25 » Sat Sep 17, 2011 1:42 pm

Visual OMP is packed full of features that make it a very powerful virtual laboratory on your PC Quickly and easily simulate DNA and RNA experiments on your desktop computer with an easy-to-use Windows interface.
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Re: VISUAL OMP

Postby albertodegama » Mon Dec 12, 2011 8:45 am

Advanced Parameters for Designs

For a description of all parameters press F1 on the probe/primer design tab and go to the help-page about the advanced parameters.

Choose a strategy (last column of design-row) which best matches your design. “Balanced” is recommended for normal probe or PCR primer design.

Review the parameters and change them to your needs if necessary. The most adjusted parameters in general are:

Oligo size, the length of the primer/probe you are going to design. If you do not care too much about its length, maintain minimum and maximum values and change the values of the weighting factors, if you like. For example, a primer of length 20 may have min=18 and max=22 with weight factors as 0, 0 meaning that any primer of length between 18 to 22 nucleotides will be weighted the same.

The same applies to amplicon size in case of primer pair designs. For example, if the intended amplicon is between 100-200 nucleotides long, then you can adjust the minimum and maximum values as such and change the weight factors to 0, 0 as well.

Duplex Tm is the melting temperature of the intended heterodimer. This needs to be set a couple of degrees (5 to 10) higher than the assay annealing temperature, so that heterodimer-concentrations at the assay-temperature will be at a maximum.

Solution distance, one of the parameters on the right side of the screen. This value indicates the minimum number of nucleotides which are apart from each other in a set of design solutions. For example, setting it to 3 means that if a primer#1 starts from nucleotide #1 on your target, then the next primer solution will have a minimum starting point at target-nucleotide #4. For designs which are not very restricted, the default of 3 is good and will save computational time. But for difficult designs where you are restricted to a certain region for example, it’s recommended to decrease the value of the solution distance to 1. This way more potential probes/primers will be considered.
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albertodegama
 
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Re: VISUAL OMP

Postby Mikael Kubista » Wed Dec 14, 2011 10:18 pm

TATAA Biocenter is selling Visual OMP in Europe and also provides training. See: http://www.tataa.com/products/Primer-de ... ducts.html for more info!

Good luck
Mikael Kubista
 
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