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by com.seqbench

Restriction sites

restriction_sites
Read-onlyIdempotent

Find restriction enzyme recognition sites in a DNA sequence.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
enzymesNoEnzyme names to scan; omit to scan the curated common-enzyme set. A name is resolved against the curated set, the Type IIS cutters and the generated REBASE table, case-, punctuation- and HF/v2-variant-insensitively, so "ecori", "EcoRI-HF", "BsaI" and "BsmFI" all resolve. A name that resolves to nothing is REJECTED rather than dropped — an unscanned enzyme reported as having no sites is indistinguishable from one that genuinely does not cut.
circularNoTreat the sequence as circular (plasmid) so sites spanning the origin are found.
sequenceYesNucleotide sequence (raw or FASTA; IUPAC accepted).

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Changed1 schema field changed
    • changedInput schema / properties / enzymes / description
      Previous value: -"Enzyme names to scan; omit to scan all curated enzymes."New value: +"Enzyme names to scan; omit to scan the curated common-enzyme set. A name is resolved against the curated set, the Type IIS cutters and the generated REBASE table, case-, punctuation- and HF/v2-variant-insensitively, so \"ecori\", \"EcoRI-HF\", \"BsaI\" and \"BsmFI\" all resolve. A name that resolves to nothing is REJECTED rather than dropped — an unscanned enzyme reported as having no sites is indistinguishable from one that genuinely does not cut."
  2. Changed1 schema field changed
    • addedInput schema / properties / circular
      Added value: +{
+  "default": false,
+  "description": "Treat the sequence as circular (plasmid) so sites spanning the origin are found.",
+  "type": "boolean"
+}
  3. First observed

TDQS

B3.3/5.0
Behavior3/5

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

The description does not contradict the annotations; readOnlyHint and idempotentHint already communicate that this is a safe, read-only operation. It adds no additional behavioral context such as output shape or edge cases, but the annotations carry most of that burden, leaving it minimally adequate.

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?

A single sentence with no filler; the verb and object are front-loaded. It is appropriately sized for the simple operation it describes.

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

Completeness3/5

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

The schema and annotations cover the parameters and safety profile, so an agent can invoke the tool correctly. What is missing is guidance on selecting this tool over similar siblings and any indication of what the result structure looks like, since there is no output schema.

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

Parameters3/5

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

All three parameters have schema descriptions, so the baseline is 3. The tool description itself says nothing about parameters, but the schema compensates fully; therefore no penalty or extra credit beyond baseline is warranted.

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

Purpose4/5

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

The description uses a specific verb ('find') and a well-defined resource ('restriction enzyme recognition sites in a DNA sequence'), so the core operation is clear. It does not, however, contrast with sibling tools such as diagnostic_digest or double_digest, so it misses some differentiation that would make it a 5.

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

Usage Guidelines2/5

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

The description gives no guidance on when to use this tool rather than a sibling, nor any exclusions or prerequisites. While the schema explains the optional enzyme list and circular mode, it does not address selection among related restriction/digest tools.

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

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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