workbench

Verify a claimed construct

verify_construct

Read-onlyIdempotent

Re-derive a construct's insert from the PCR (template + primers) claimed to have produced it, then check — independently of that claim — whether the expected insert actually appears (either orientation) in the claimed final construct, at what identity, and with exact mismatch positions if not. Optionally also checks for a premature stop in a declared reading frame. Primers may carry a non-templated 5' tail (a restriction site, a Gibson arm, a tag): a construct missing ONLY tail bases still passes, since that is exactly what digesting a tailed amplicon removes before ligation — see match.templateCoveragePct and match.unalignedIsTailOnly, and note the pass does not establish that the right enzyme made the cut. This re-derives from the claim's own stated inputs; it does not review the claim's prose.

Input Schema

TableJSON Schema

Name	Required	Description
`insertTemplate`	Yes	PCR template the insert was amplified from.
`claimedConstruct`	Yes	The final sequence claimed to have been built.
`templateCircular`	No	Treat insertTemplate as circular (e.g. amplifying from a plasmid).
`expectedFrameStart`	No	1-based position in claimedConstruct where the intended reading frame begins. If given, flags a premature stop before the end of the aligned insert region.
`insertForwardPrimer`	Yes	Forward primer used to amplify the insert, 5'→3'.
`insertReversePrimer`	Yes	Reverse primer used to amplify the insert, 5'→3'.
`maxPrimerMismatches`	No	Mismatches tolerated per primer during PCR prediction (0–10).

TDQS

A4.7/5.0

Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Beyond the readOnly and idempotent annotations, the description discloses important behavioral nuances: tail-bases-only mismatches are allowed, the pass does not confirm the correct enzyme was used, and it references output fields (match.templateCoveragePct, match.unalignedIsTailOnly). This is rich additional context.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is dense but every sentence contributes: core action, optional frame check, tail handling caveat, and the non-review of prose. It front-loads the primary purpose and expands into edge cases, earning its length.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Despite no output schema, the description conveys the verification logic, acceptable mismatch interpretation, optional frame check, and output field hints. This is sufficient for an agent to decide whether and how to invoke the tool correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so baseline is 3. The description adds value by explaining how primer tails are interpreted and that expectedFrameStart flags premature stops, giving deeper meaning to those parameters than the schema alone. This pushes it to a 4.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb ('re-derive', 'check') and resource (construct insert from PCR), and clarifies the independence of the verification from the claim's prose. This distinguishes it from other verification tools like verify_assembly without needing to open the schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Provides clear context: use when a claimed construct needs verification against PCR template and primers. It also gives an explicit exclusion ('it does not review the claim's prose'), but it does not name specific alternative tools or conditions for when to prefer them, so it falls short of a full 5.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

All workbench tools Inspect

Try in Browser

RayrunBuild, deploy, and operate MCP servers without becoming an infrastructure team.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.

TDQS

A3.6/5.0

Disambiguation4/5

Most tools have highly specific purposes (e.g., crispr_grna_design vs base_editing_design vs prime_editing_design). However, there is some overlap in sequence analysis tools (characterize_sequence, sequence_report) and plasmid annotation tools (plasmid_annotate vs plasmid_deep_annotate) which could cause confusion.

Naming Consistency3/5

The naming pattern is largely consistent with snake_case verb_noun or noun_descriptor (e.g., primer_design, plasmid_annotate, fastq_trim). However, there are exceptions like 'batch', 'workflow', 'gc_content', and 'cloning_diagnose' which don't follow the verb_noun pattern consistently. Also, some names are phrases like 'golden_gate_from_parts'.

Tool Count2/5

With 101 tools, this server is extremely large and likely overwhelming for agents. Even for a comprehensive bioinformatics toolkit, this exceeds a manageable scope, risking agent confusion and inefficient tool selection. A more modular approach would be advisable.

Completeness4/5

The tool surface covers a wide range of bioinformatics workflows including sequence analysis, primer design, cloning, CRISPR, NGS, expression analysis, and data export. There are minor gaps such as lack of a dedicated protein structure prediction tool and limited off-target genome coverage, but overall the set is impressively complete for its domain.

Resources

Need Help?