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Jean — Molecular Biology & Genomics

rps_blast_smart

Read-only

rpsblast, run on this machine: find conserved domains in a protein against NCBI's SMART domain models (1,011 PSSMs from CDD).

Input Schema

NameRequiredDescriptionDefault
_filesNoThe 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.
evalueNoreport alignments with E at most this (`-evalue`); BLAST's default is 10.
sourceNowhere the SMART database is read from: 'bundled' (a byte-identical copy of NCBI's file) or 'ncbi' (NCBI's FTP site, now). Advanced.bundled
proteinYesthe protein, one-letter codes; wire it from translate_sequence or read it off a CDS.
_subjectNoThe 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.
max_target_seqsNomost domain models reported (`-max_target_seqs`).

Output Schema

NameRequiredDescriptionDefault
countYesdomain models hit
domainsYesevery SMART domain hit, best first: accession, shortName, title, profileLength and each HSP's residue coordinates, model coordinates, score, bits, E-value, identities, positives, gaps and aligned strings

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.7/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is covered. The description adds real value on top: it states the search executes locally on this machine and pins the database provenance and size (1,011 PSSMs from CDD), which tells the agent what corpus the hits come from and that the run is offline.

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?

A single dense sentence with no wasted words, front-loading the tool name and the core action. The colon-and-clause structure is slightly telegraphic but readable and efficient.

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?

With an output schema present, return values need not be explained, and all six parameters are fully documented in the schema. The description covers what the tool does, where it runs, and which database it uses; only the sibling differentiation is left implicit.

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%, with every parameter including evalue, max_target_seqs, source and protein already documented in the schema itself. The description adds no parameter meaning beyond what the schema states, so the baseline 3 applies.

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?

The description names a specific tool (rpsblast), a specific action (find conserved domains in a protein), and a specific database (SMART domain models, 1,011 PSSMs from CDD). The database detail implicitly distinguishes it from the rps_blast_cdd and rpstblastn_smart siblings, though it never names them explicitly.

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 resource named - an agent can infer this is the SMART-domain search - but the description gives no explicit when-to-use, when-not-to-use, or which sibling to pick for CDD versus SMART versus translated searches. 'Run on this machine' hints at a local vs remote distinction but that is never turned into 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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