The planner assumes a Bio-Rad Precision Plus Protein Dual Color ladder (#1610374). If you run a different ladder its band sizes will not match, and the positions will be wrong — see the caution at the end of this section.
Band positions come from one of three sources. Only the last is grounded in your gel, and the tool always shows which one is active.
Rf is taken as linear in log10(MW) across the gel's resolving range, the standard SDS-PAGE relationship, anchored so the top of the range sits at Rf 0.15 and the bottom at Rf 0.85, then passed through a logistic squash (k = 4) so proteins outside the range compress toward the well or the dye front instead of leaving the gel. The ranges used — 15% = 10–40, 12% = 20–80, 10% = 40–120, 8% = 60–200 kDa — are conventional rule-of-thumb figures for handcast Tris-glycine gels.
Rf values measured by pixel analysis of Bio-Rad's published Criterion Tris-HCl migration chart, normalised as (band − well bottom) / (gel bottom − well bottom), across all eleven columns. Between tabulated bands the tool interpolates linearly in log10(MW); beyond them it extrapolates and says so. A band missing from a column means Bio-Rad's chart does not show it — it has run off that gel.
The chart also has no 8% or 12% column, so those recipes map to the nearest available 7.5% and 12.5%.
Discards every model above and fits distance = A + B·log10(MW) by ordinary least squares to distances you measured off your own Ponceau, reporting R² and residuals, with per-band control over what enters the fit.
Real ladders stop being log-linear at the extremes — the largest and smallest bands compress. Including them drags the fitted line and worsens the prediction exactly where your targets sit. If R² is low, untick the bands outside the gel's resolving range and refit.
Each target gets a protected zone: its band extent plus your band-clearance margin above and below. Targets whose zones overlap cannot be separated and are merged into one strip. Cuts are then placed midway between consecutive zones, and any cut that would leave a strip shorter than your minimum height is dropped.
Cut positions are reported in millimetres from the top of the resolving gel, and also relative to the nearest ladder band — easier to use at the bench than a ruler origin. Drag any cut on the gel to override it.
Bio-Rad Precision Plus Protein Dual Color Standards #1610374: ten bands at 250, 150, 100, 75, 50, 37, 25, 20, 15 and 10 kDa. The 75 and 25 kDa bands are pink, the other eight blue. Band identities were confirmed against the vendor product image.
Every preset molecular weight was read from that antibody's own
Cell Signaling Technology product page, from the "MW (kDa)"
specification field, and is quoted verbatim. Each button's tooltip carries the catalog number the value came
from, so any of them can be rechecked at cellsignal.com/products/<cat>/datasheet.
None were written from memory.
Where a datasheet lists two bands — Lamin B1 68 and 45, Lamin A/C 70 and 28, Caveolin-1 21 and 24 — the preset uses the full-length species and the tooltip names the other, because a cleavage product you didn't plan for is a good way to lose a strip.
Controls are grouped by subcellular fraction. Pick one from the same fraction as your target — a cytoplasmic control says nothing about loading in a nuclear prep.
Enter the observed molecular weight — what the vendor says you will actually see on a blot — not the weight calculated from the sequence. Observed weights shift with glycosylation, phosphorylation, multimerisation, species and cell type. Always prefer the number on the datasheet of the antibody actually in your freezer. For proteins that run as a doublet or a smear, enter both bounds and the tool will protect the whole span.
Your experiment never leaves your browser. Targets, molecular weights, antibodies, gel settings and calibration measurements are all computed locally and stored only in this browser's own storage. There is no server to send them to, no account, and no sign-in. Clearing your browser data deletes them; the Export JSON button is how you keep a copy.
The hosted site may count anonymous page views so it is possible to tell whether anyone is using
the tool. That counter records a visit and nothing else — no IP address, no cookies, and nothing about your
work. It never runs on a downloaded copy or when the installed app is used offline. If you would rather not
be counted at all, download index.html and open it directly; it is the complete tool and makes
no network requests whatsoever.
You are running BlotPlanner v. Please quote that in any bug report — the footer of any printout and any exported plan carries it too.
Built by Roman Caceres
(@Roman-Caceres). Source code, version history and updates live at
github.com/Roman-Caceres/BlotPlanner.
Bug reports, requests for other ladders, and notes on what the tool got wrong at your bench are all welcome through the same link.
This is a planning aid, not a measurement. It is provided as-is, without warranty of any kind, and the author accepts no liability for experimental loss arising from its use. Verify every cut position against your own stained membrane before scoring it.
Bio-Rad, Precision Plus Protein, Cell Signaling Technology and all product names are trademarks of their respective owners. This tool is independent and is not endorsed by, affiliated with, or produced in partnership with any of them.
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