Beacon Designer is an application that can help you design PCR primes, usually used by molecular biologists in their studies. This application comes packed with all the necessary features that you’d expect to find in any professional software solution that deals with such a task.
The user interface may seem a bit overwhelming at a first glance, but this is only because this tool packs so many useful options. There are several designs available and you can opt for a beacon, FRET, HRMA, MethyLight TaqMan, Scorpions, SYBR or TaqMan.
It bundles an automatic adjustment feature that can help you select the stem of appropriate length for creating an optimal beacon.
Moreover, Beacon Designer can create molecular beacons for detection of wild and mutant alleles, and design beacons and primers for multiplex reactions. It provides accurate hairpin Tm calculation, and is able to display a graphical view of the designed beacons.
The program allows users to generate different beacons and primers, and you can save the data as projects.
It is possible to select the items that should be included in the final results report for beacons and primers, such as quality, position, length, and others. The results can be exported to XLS file format.
You can also sort primers by making the program display the sense and antisense primer, and product on the basis of rating, position, length, Tm, and others. The program also bundles a print preview feature, and it is possible to zoom in or out of different pages.
Beacon Designer is able to design optimal primers based on standard reaction conditions, and you can view and change the conditions, such as nucleic acid concentration, temperature for free energy calculation, and others.
In conclusion, Beacon Designer is an application that can help you design primes and beacons efficiently. Although, it may take some time to get used to working with this tool, a help menu is included, so you can understand the functions of each dedicated parameter.