workbench

Characterize sequence

characterize_sequence

Read-onlyIdempotent

One-paste 'tell me everything': auto-detects DNA/RNA/protein, then reports composition, ORFs, single-cutter enzymes, end primers or protein properties, plus a BLAST link.

Input Schema

TableJSON Schema

Name	Required	Description
`maxOrfs`	No	Maximum number of ORFs to return, longest first.
`minOrfAa`	No	Minimum ORF length in amino acids (nucleotide input only).
`sequence`	Yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
`endPrimerLength`	No	Length of the naive end primers taken from each end.

TDQS

A4/5.0

Behavior4/5

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

Annotations already indicate readOnlyHint and idempotentHint. The description adds behavioral context by listing the types of analyses performed (composition, ORFs, enzymes, etc.), which helps the agent understand the scope. No contradictions with annotations.

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 a single, concise sentence that front-loads the key purpose and lists the outputs efficiently. No unnecessary words.

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

Completeness4/5

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

Given the tool's complexity (multiple analysis types), the description covers the main outputs. However, it does not mention the output format or any caveats (e.g., optional parameters). Annotations and schema cover safety and parameter details, so overall completeness is good but not perfect.

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?

Schema description coverage is 100%, so the parameter meanings are well-documented in the schema. The description adds no additional parameter semantics beyond what is in the schema, so baseline score is appropriate.

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 clearly states that the tool auto-detects sequence type and provides a comprehensive characterization including composition, ORFs, enzymes, primers, protein properties, and a BLAST link. This effectively differentiates it from siblings that focus on specific aspects like find_orfs or protein_properties.

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

Usage Guidelines3/5

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

The description implies the tool is for comprehensive analysis ('One-paste tell me everything'), but does not explicitly state when to use it versus alternatives or when not to use it. Sibling tools provide context, but the description lacks direct guidance.

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

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