SeqCode MCP
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| list_namesA | Retrieve a paginated list of names from the SeqCode Registry. Each entry contains id, name, url and uri. Optionally filter by status: 'public', 'automated', 'SeqCode', 'ICNP', 'ICNafp', or 'valid'. |
| get_nameA | Retrieve detailed information about a specific name by its numeric ID. Returns rank, status, etymology, description, classification, nomenclatural type, proposed_in publication, and more. |
| list_genomesB | Retrieve a paginated list of genomes registered in the SeqCode Registry. |
| get_genomeA | Retrieve detailed information about a specific genome by its numeric ID. Includes accession, kind (isolate/MAG/SAG/enrichment), genomic features (completeness, contamination, GC content, rRNA genes, tRNAs, N50, contigs, assembly length, etc.), associated names, and strain info. |
| list_type_genomesC | Retrieve a list of type genomes from validly published names and their corresponding names. |
| list_registersB | Retrieve a paginated list of validated register lists from the SeqCode Registry. |
| get_registerB | Retrieve detailed information about a specific register list by its accession. Includes submitter, authors, DOI, effective publication, and the list of names in the register. |
| list_publicationsB | Retrieve a paginated list of publications referenced in the SeqCode Registry. |
| get_publicationA | Retrieve detailed information about a specific publication by its numeric ID. Includes citation, DOI, title, journal, type, abstract, authors, associated names, and subjects. |
| list_authorsC | Retrieve a paginated list of publication authors from the SeqCode Registry. |
| get_authorA | Retrieve detailed information about a specific author by their numeric ID, including their list of publications. |
| list_journalsA | Retrieve a paginated list of publication journals from the SeqCode Registry. |
| get_journalA | Retrieve detailed information about a specific journal by name, including its list of publications. |
| list_subjectsC | Retrieve a paginated list of publication subjects from the SeqCode Registry. |
| get_subjectA | Retrieve detailed information about a specific publication subject by its numeric ID, including associated publications. |
| get_strainB | Retrieve detailed information about a specific strain by its numeric ID. Includes strain numbers, typified names, genomes, and strain info DOIs. |
| search_seqcodeB | Search the SeqCode Registry for names, genomes, publications, authors, or subjects. Returns a list of matching items with id, name, url, and api_url for each result. Use the specific 'get_*' tools for detailed information about individual results. |
| check_api_statusB | Check that the SeqCode Registry REST API is accessible. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 18 tools
The list_/get_ pairs for each entity are clearly distinct, and the search tool is explicitly scoped as cross-entity text search. Minor overlap exists because search_seqcode can return names, genomes, etc. that also have dedicated list tools, and list_type_genomes is a specialized subset of list_genomes/list_names, but descriptions clarify the boundaries.
All tools follow a predictable snake_case verb_noun pattern: list_publications/get_publication, list_names/get_name, etc. The few non-paired tools (list_type_genomes, search_seqcode, check_api_status) still conform to the same style. No mixed conventions or confusing variations.
With 18 tools, the set is slightly above the ideal 3-15 range, but the count is justified by the registry's breadth: eight entity types each need a list and get operation, plus search and status checks. No tool feels redundant or purely filler.
The server provides comprehensive read-only coverage for names, genomes, publications, authors, journals, subjects, and registers via list+get pairs. However, strains only have get_strain without a list_strains, limiting discoverability, and type genomes lack a dedicated get tool (though get_genome covers them). These are minor gaps for a read-only registry API.