Run a Virtual Gel Simulation on Genome Compiler
Gel electrophoresis is an analysis method implemented in all disciplines of life sciences. The results of gel electrophoresis indicate the relative sizes of fragments, which is useful for restriction mapping and analyzing PCR fragments. The standard method, explained by Olwen Reina in this bitesizebio article, uses an electric current to move charged molecules through a gel made of agar or polyacrylamide. In a process called sieving, the larger fragments move slowly through the gel while the smaller fragments move faster and farther as they travel more easily through the gel’s pores. Thus, the fragments end up forming distinct bands in order of length, resembling ladders.
Genome Compiler has introduced a virtual gel tool so you can run an online simulation of gel electrophoresis on your plasmids designed in the software. You can then save the virtual gel as a picture, and use it to compare the physical gel electrophoresis of your digested sequences with the simulated results to check for any errors in the physical experiment.
Running a gel simulation in Genome Compiler is very simple.
- After you’ve conducted your virtual cloning experiment, select the “digest” icon along the top in the toolbar. The “run digest” dialogue will appear, from which you can choose your restriction enzymes from a list of preset options. You have the option to filter the list by certain criteria such as cut pattern, compatibility, and number and location of cuts.
- When you have selected your preferred enzymes, select Run Digest at the bottom of the prompt. A digest window will appear showing the length of your fragments. You can also specify whether your project topology is circular or linear and the fragments generated will adjust accordingly. To view the gel, select Gel Simulation.
- You then have the option to choose a ladder with which to run your gel. Your fragments will always be arranged according to the ladder you choose.
- Hovering over a fragment will display its length.
- If any fragments are outside of the gel ladder limits, a warning will appear at the bottom of the ladder. This information can help you choose a better ladder for your specific experiment.
- Finally, save your virtual gel as a picture on your computer to later use to verify the accuracy of your physical gel electrophoresis.
This feature allows you to check your experiments without resorting to the traditional method of mapping by hand. To get started with some other great features of Genome Compiler, check out this tutorial video and this webinar.