Skip to main content
Glama

Enumerate candidate ORFs

computase_enumerate_orfs
Read-onlyIdempotent

Find all open reading frames (ORFs) in a nucleotide sequence by scanning all six reading frames, with adjustable start/stop codon requirements and genetic code tables.

Instructions

Enumerate bounded candidate ORFs across all six reading frames.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sequenceYesRaw nucleotide sequence or one FASTA record; IUPAC codes are accepted. The normalized sequence is limited to 5,000,000 nucleotides.
table_idNoNCBI genetic-code table identifier.
max_resultsNoMaximum returned candidates.
require_stopNoRequire an in-frame terminal stop codon.
start_codonsNoAllowed start-codon policy.table-starts
min_length_ntNoMinimum nucleotide span including stop.
include_nestedNoReport starts nested before the same stop.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
noteNoScientific interpretation boundary.These are candidate ORFs, not gene predictions.
orfsYesCandidate ORFs in deterministic coordinate order.
truncatedYesWhether candidates were omitted by max_results.
parametersNoEffective operation parameters, excluding the input sequence.
total_foundYesTotal candidates found before result limiting.
computase_versionNoComputase version used for the computation.0.1.1
coordinate_systemNo0-based-half-open
Behavior3/5

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

Annotations already declare readOnlyHint=true, idempotentHint=true, and destructiveHint=false, so the agent knows it's safe. The description adds 'bounded' and 'all six reading frames,' which clarifies output scope but not additional behavioral traits like output format or limit handling, which are covered by the schema and output schema.

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 sentence with an action-first structure, no redundant statements, and fully captures the tool's essence.

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 rich schema, output schema, and clear annotations, the one-sentence description is sufficient to convey the tool's role. It could optionally mention that this is for analysis after sequence input, but not essential. Overall complete for an agent to select and invoke correctly.

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?

The input schema has 100% coverage, with descriptions for all 7 parameters. The tool description adds no parameter-specific information, so it relies entirely on the schema. Baseline 3 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 a specific verb ('Enumerate') and resource ('bounded candidate ORFs') with the scope of 'all six reading frames,' distinguishing it from sibling tools like motif scanning or translation.

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 ORF discovery but does not explicitly specify when to use it over alternatives like computase_scan_motif or translate_sequence. It provides clear context (enumerating ORFs) but no exclusions or alternative recommendations.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/madhusudan-kulkarni/computase'

If you have feedback or need assistance with the MCP directory API, please join our Discord server