sds-gel-review

name	sds-gel-review
description	Review SDS-PAGE or protein purification gel images using DNA sequence, protein sequence, base-pair length, expected protein size, and lane labels. Use when the user wants to judge whether a gel ran well, whether the main band matches the expected product, or whether there may be impurities, degradation, aggregation, or low expression.

SDS-Gel Review

Use this skill when the user provides a gel image plus any of:

• DNA sequence
• protein sequence
• coding sequence length in bp
• expected protein size in kDa
• tag, construct, host, purification step, or lane labels

This is an interpretation skill, not a definitive assay. Distinguish what is directly observed from what is inferred.

Main goal

Given a gel image and partial sequence/context, produce a practical lab-style judgment:

• did the gel run cleanly or poorly
• is there a plausible main band
• does the main band roughly match the expected target
• are there obvious impurities, degradation, smearing, or aggregation
• what extra information would most improve confidence

Inputs to request or infer

Collect as many of these as possible before judging:

• gel image
• whether the image is SDS-PAGE, western blot, or native gel
• DNA sequence or protein sequence
• if only bp is given, whether it is coding sequence length
• expected protein name
• expected molecular weight in kDa
• expression host
• tag or fusion partner
• purification step or lane meaning
• whether reducing conditions were used
• whether a ladder is visible

If some are missing, continue with a lower-confidence interpretation.

How to reason

1. Normalize the sequence information

• If the user provides a protein sequence, use it directly.
• If the user provides a DNA sequence, treat it as coding sequence only if the context supports that.
• If the user provides only bp length, estimate protein length as bp / 3 aa only when it is likely a coding region.
• Estimate theoretical protein mass with the rough rule 110 Da per amino acid.
• Convert to kDa and note that tags, signal peptides, cleavage, glycosylation, oligomerization, and unusual composition may shift apparent migration.

2. Read the gel image conservatively

Inspect the image for:

• lane count and lane boundaries
• visible labels above or below lanes
• presence or absence of ladder
• strongest band in each relevant lane
• approximate relative migration of the strongest band
• extra lower bands suggesting degradation
• extra upper bands suggesting dimers, aggregates, uncleaved fusion, or contaminants
• smearing, overloaded lanes, distorted fronts, or uneven running
• enrichment or loss across purification lanes if the labels indicate flow-through, wash, elution, pellet, or lysate

If the ladder is missing, use labeled lane order and relative migration only. Do not invent exact kDa values.

3. Compare expectation vs observation

Decide whether the image most supports one of these:

• likely target band at approximately expected size
• possible target band but confidence limited
• target band not clearly visible
• strong expression but poor purity
• purified sample but with degradation
• aggregation or high-MW species likely
• gel quality too poor for a reliable call

4. Explain confidence

Confidence is higher when:

• ladder is visible
• expected protein size is provided
• lane labels are clear
• construct/tag information is available
• the gel has multiple purification steps that tell a consistent story

Confidence is lower when:

• only bp count is provided
• ladder is absent
• lane labels are missing
• image quality is low
• the construct may include tags or cleavage not described

Important guardrails

• Never claim a precise molecular weight from the image when no ladder is visible.
• Never claim a band is definitely the target protein from DNA length alone.
• Clearly separate:
  • Observation: what the image visibly shows
  • Inference: what might explain it
• If the image quality or metadata are insufficient, say so plainly.
• Prefer practical lab wording over overconfident structural biology language.

Output format

Use this structure:

Overall judgment

• One short paragraph on whether the gel looks interpretable and whether the target seems present.

What I can directly see

• lane pattern
• strongest band(s)
• impurities, smear, aggregation, or degradation
• whether purification appears to improve the sample

Expected size estimate

• from protein sequence, DNA sequence, or bp count
• state assumptions clearly

Does the observed band roughly match?

• yes / maybe / unclear / no
• explain why

Main concerns

• 1 to 3 likely issues only

What would help next

• ask for the smallest missing item that would improve confidence, such as:
  • ladder annotation
  • lane labels
  • exact coding sequence length
  • tag/fusion information
  • expected kDa
  • original uncropped image

Practical heuristics

• Approximate aa count from coding sequence: bp / 3
• Rough protein mass: aa * 110 Da
• His-tag or small peptide tags usually shift size only slightly
• Large fusion tags can meaningfully shift migration
• Smear below the main band often suggests degradation or proteolysis
• Signal near the top or stacking boundary can suggest aggregation or incomplete denaturation
• A very thick single band with little else may still reflect overloading

Example task types

• "Here is a DNA sequence and SDS-PAGE image. Did my purification work?"
• "This construct is 978 bp. Does the main band in this gel make sense?"
• "I expect a 42 kDa protein. Which lane looks best?"
• "No ladder on this gel, but the lanes are labeled lysate, wash, elution. Please judge whether the elution looks clean."