BioHarbor

find_orfs

Identify open reading frames from DNA or RNA on both strands, returning the longest ORFs with coordinates and saving all ORFs to a FASTA file.

Instructions

Find open reading frames (ATG to stop) on both strands.

Returns the longest ORFs in DNA/RNA with coordinates (1-based, on the forward strand) and writes all ORFs to a FASTA file.

Input Schema

TableJSON Schema

Name	Required	Description
`top_n`	No	How many of the longest ORFs to return.
`min_aa`	No	Minimum ORF length in amino acids (1 = any ORF).
`sequence`	Yes	A raw sequence or FASTA text (one or more records).
`both_strands`	No	Also search the reverse complement.

Output Schema

TableJSON Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 7, 2026

TDQS

B3.2/5.0

Behavior3/5

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

No annotations provided, so description carries full burden. It does disclose a side effect—writing all ORFs to a FASTA file—and mentions returned coordinates. However, it omits whether the file write overwrites existing files, required permissions, runtime characteristics, or whether the operation is otherwise read-only. Partial behavioral coverage.

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

Conciseness4/5

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

Two sentences, front-loaded with purpose. The second sentence efficiently covers return format and side effect. No redundant or filler text.

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?

Output schema exists, so return values need not be explained, though the description does so anyway. Missing usage guidelines and partial behavioral disclosure (e.g., file overwrite behavior) leave the definition incomplete for a tool with no annotations.

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 schema already documents all four parameters. The description adds little beyond the schema—'both strands' and 'longest ORFs' map directly to parameters but without extra syntax or format details. Baseline 3 is appropriate.

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?

States a specific verb and resource: 'Find open reading frames (ATG to stop) on both strands.' Clear what the tool does, but does not explicitly distinguish from siblings like translate_sequence or seq_stats.

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?

No when-to-use guidance, no alternatives named, no prerequisites mentioned. The description only implies usage through the purpose statement.

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

Deploy Server