Jean — Molecular Biology & Genomics

rpstblastn_smart

Read-only

rpstblastn, run on this machine: find conserved domains in DNA by searching all six reading frames against NCBI's SMART domain models (1,011 PSSMs from CDD).

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "rpstblastn_smart"
  }
}

Input Schema

Name	Required	Description	Default
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`evalue`	No	report alignments with E at most this (`-evalue`); BLAST's default is 10.
`source`	No	where the SMART database is read from: 'bundled' (a byte-identical copy of NCBI's file) or 'ncbi' (NCBI's FTP site, now). Advanced.	bundled
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
`sequence`	No	the DNA to search, 5′→3′; leave empty to search the open record. Both strands are searched.
`genetic_code`	No	NCBI genetic code used to translate the six frames (`-query_gencode`).
`max_target_seqs`	No	most domain models reported (`-max_target_seqs`).
`comp_based_stats`	No	composition-based statistics: 1 on (the default, Schäffer et al. 2001), 0 off.

Output Schema

Name	Required	Description	Default
`count`	Yes	domain models hit
`domains`	Yes	every SMART domain hit, best first: accession, shortName, title, profileLength and each HSP's nucleotide coordinates (1-based, to < from on the minus strand) and frame, model coordinates, score, bits, E-value, identities, positives, gaps and aligned strings

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A3.7/5.0

Behavior4/5

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

Annotations already cover safety (readOnlyHint=true, openWorldHint=false, destructiveHint=false), so credit goes to what the description adds: it clarifies execution is local ('run on this machine') and discloses database provenance and size (1,011 PSSMs from CDD), including the bundled-vs-NCBI choice via the source parameter. It stops short of noting runtime cost or that six-frame translation can produce many hits.

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 front-loaded sentence with the program name first, then the purpose and the reference database, and no wasted words. Every clause adds information.

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?

With an output schema and fully documented parameters, the mechanics are covered. The missing piece relative to tool complexity is routing guidance among several very similar domain-search siblings, which the description leaves to the agent to infer from the tool name alone.

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 baseline is 3. The description only touches database provenance implicitly; it adds no syntax, format, or interpretation guidance (e.g., evalue meaning) beyond what the schema already documents.

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?

Specific verb+resource: 'find conserved domains in DNA by searching all six reading frames against NCBI's SMART domain models (1,011 PSSMs from CDD)' tells an agent exactly what the tool does. It does not, however, name or disambiguate itself from the near-identical siblings rps_blast_smart, rps_blast_cdd, and delta_blast_smart, which an agent would need to distinguish.

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?

Usage is only implied by the phrasing 'find conserved domains in DNA'; there is no explicit statement of when to pick this over rps_blast_smart (protein query), rps_blast_cdd (broader CDD), or blast_search. No exclusions or prerequisites are given.

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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