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.
🔒 Nothing you paste is logged or stored
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 — the same symptom always gives the same causes and the same checks — 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, so the same symptom always yields the same answer. 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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