Gel Electrophoresis Troubleshooter — Symptom Guide
Diagnose gel problems (no bands, smearing, wrong size, primer-dimer, degradation) with a fully deterministic symptom guide that links to the right SeqBench tools.
🌐 This guide runs entirely in your browser — no upload, no network call, nothing sent to SeqBench's server.
Pick what your gel looks like — no bands, a smear, a band at the wrong size, a primer-dimer, or degraded input — and get the likely causes with concrete next checks, each linking straight into the SeqBench tool that tests it (Primer Tm, In-silico PCR, Oligo Analyzer, Virtual Gel, FASTQ QC). The guide is fully deterministic: no AI, no network call, no cost, and it drives troubleshooting back into the calculators rather than dead-ending on a guess.
Pick what you see on the gel. Each cause links to the SeqBench tools that check it — fully deterministic, no AI, works offline.
The expected lane is empty (loading dye ran, but no DNA is visible).
- Re-check primer Tm and that both primers actually anneal to the template.→ Primer Tm
- Confirm the primers produce an amplicon on this template in silico (right binding sites, sensible size).→ In-silico PCR
- Check primers aren't dominated by dimers/hairpins that outcompete the target.→ Oligo Analyzer
- Verify template concentration and integrity (a no-template or degraded-template lane looks identical to a failed reaction).
- Confirm polymerase, dNTPs and Mg2+ were all added and not expired.
- Check run time/voltage vs. fragment size and that stain (e.g. SYBR/EtBr) was present and imaged on the right channel.
How to use the Gel Troubleshooter tool
- 1Select the symptom that matches your gel.
- 2Read the likely causes and follow each check's link into the matching SeqBench tool (e.g. re-check primer Tm, recompute expected amplicon size, screen for primer-dimers).
- 3Re-run the gel once you've addressed the most likely cause.
Frequently asked questions
Is this AI-powered?
No — it is a fully deterministic decision tree (symptom → likely causes → concrete checks) built from standard gel/PCR troubleshooting knowledge. It runs entirely in your browser with no network call and no cost, and each check links into the SeqBench tool that actually tests it.
Why isn't there an option to upload a photo of my gel?
That isn't offered. This tool is a checklist, not an image-analysis feature — pick your symptom and follow the checks it links to.
Which SeqBench tools does it link to?
Primer Tm, In-silico PCR, Oligo Analyzer, Primer Designer, Virtual Gel, and FASTQ QC, depending on the symptom and likely cause — each is the tool that actually re-checks that specific thing (primer Tm/binding, expected product size, primer-dimer risk, input read quality, and so on).
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