EMSA Analyzer
EMSA Kd calculator — free online gel shift analysis
Tired of ImageJ? Try this instead.
You know the routine: draw a rectangle for every lane, plot the profiles, close off each peak by hand, click it with the wand, paste the areas into a spreadsheet, work out fraction bound, then move to another program to fit the curve. For every gel. And the next time you do it, the baseline lines land somewhere else.
EMSA Analyzer does the whole thing in one place. Drop in the gel image, check the lanes and bands it finds, type in your protein concentrations and read off Kd with a 95% confidence interval. Quick and easy — moments rather than minutes — and the same regions give the same Kd every time.
What it does
Reads your gel as it is
JPEG, PNG or 16-bit TIFF straight from the imager, at full bit depth. Crop and straighten in the app.
Finds lanes and bands
Auto analyse places lanes and the bound and free windows. You stay in control: every region can be dragged, added or removed.
Handles the background properly
A rolling-ball pass over the whole gel, then a smooth per-lane baseline, with a trace view to check each lane. Void bubbles and dust with exclusion regions.
Fits the right model
Hill, hyperbolic or tight-binding (for when the probe concentration approaches Kd), with a bootstrap 95% CI and a warning if the titration didn't reach saturation.
Two ways to count binding
Bound / total, or free-probe depletion for when binding changes the label's fluorescence or the complex smears.
Compares and combines
Overlay several titrations on one normalised axis, or combine replicates into one Kd with a cross-replicate CI.
Measures any band
The Band Analyzer tab gives background-corrected intensity for any band on any gel — westerns, agarose, stained protein gels.
Publication-ready exports
Annotated gel PNG, binding-curve PNG and a CSV that records the method, model and fit parameters.
Questions
Is my gel uploaded anywhere?
No. All processing runs in your browser. The image never leaves your computer.
Do I need to install anything or make an account?
No. Open the page and drop in an image. It is free to use.
Which file formats work?
JPEG, PNG and TIFF, including 16-bit TIFF read at full depth. Bands should be dark on a light background.
How do I learn it?
The illustrated guide walks through one example gel from upload to export, and the “i” button in the app gives the short version.
How do I cite it?
Kuhlen, L. (2026). EMSA Analyzer. emsa-analyzer.com