Measuring band size on an electrophoresis gel
Scientists use DNA gel electrophoresis to separate DNA fragments by size. An essential element of almost every gel electrophoresis experiment is the use of a DNA ladder or molecular weight marker that contains fragments of known sizes (molecular weights). 
How is band size determined on an electrophoresis gel?
Comparing the migration distance of the DNA in experimental samples to the DNA ladder allows scientists to estimate the size of the DNA fragments in their samples.
In most scenarios scientists know the expected sizes of their DNA samples, so comparing to the DNA ladder allows them to estimate the size of their sample bands by eye quickly.
Sometimes, a more precise size estimate is needed. To accomplish this, a standard curve that plots the known molecular weights (in base pairs) of the DNA ladder against the log of their migration distance is created. The standard curve can then be used to interpolate the molecular weight or size of DNA fragments in experimental samples based on their migration distance.
Digital gel analysis tools
While a ruler can be used to manually measure the distance traveled by DNA bands in gel electrophoresis, most modern systems, like the blueGel Electrophoresis System, come with imaging capabilities that allow you to analyze results digitally. There are several excellent software tools for analyzing gel electrophoresis results and determining DNA band sizes. Here are some popular ones:
- ImageJ/Fiji
- Features: Free and open-source. Can measure band distances and calculate sizes using a standard curve.
- Best For: Labs with budget constraints and users comfortable with manual data input.
- Website: ImageJ
- GelAnalyzer
- Features: Free for academic use. Automatically detects lanes and bands and calculates sizes based on a DNA ladder.
- Best For: Simple, user-friendly analysis.
- Website: GelAnalyzer
