jean — Molecular Biology & Genomics

delta_blast_smart

Read-only

DELTA-BLAST, run on this machine: build a position-specific profile for a protein from the SMART conserved domains it contains, then search other proteins with it (one PSI-BLAST iteration) — more sensitive than BLASTP for distant homologs. Searches the open record's coding sequences unless subjects gives FASTA. NCBI BLAST+ 2.17.0's algorithms, checked against the deltablast program on every bundled protein. Nothing is sent anywhere.

Input Schema

TableJSON 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
`protein`	Yes	the protein, one-letter codes; wire it from translate_sequence or read it off a CDS.
`_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.
`subjects`	No	the proteins to search, as FASTA; leave empty to search the open record's coding sequences.
`threshold`	No	lowest profile word score seeded in the lookup table (`-threshold`). Advanced.
`max_target_seqs`	No	most proteins reported (`-max_target_seqs`).
`domain_inclusion_evalue`	No	conserved-domain hits with E below this build the profile (`-domain_inclusion_ethresh`).

Output Schema

TableJSON Schema

Name	Required	Description
`count`	Yes	proteins reported
`domains`	Yes	the conserved-domain alignments DELTA-BLAST built its profile from (rpsblast at the domain inclusion E-value): accession, shortName, title, and each HSP's query and model coordinates, score, bits, E-value, identities and aligned strings
`profile`	Yes	how the profile was built: domainsUsed, columnsCovered, meanObservations, and the profile's gapped lambda and kappa
`proteins`	Yes	every protein hit, best first: id, title, length, and each HSP with query and subject coordinates, score, bits, E-value, identities, positives, gaps and aligned strings

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A4.2/5.0

Behavior4/5

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

Annotations already mark it read-only, non-destructive and closed-world. The description goes beyond that by disclosing that it runs locally, pins a specific engine version (NCBI BLAST+ 2.17.0), is validated against the reference deltablast program, and that 'nothing is sent anywhere' – genuine execution context rather than restated hints.

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?

Front-loads the algorithm and its sensitivity advantage, then adds scope and locality. Efficient overall, though the validation sentence ('checked against the deltablast program on every bundled protein') is a touch verbose for the value it adds.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With an output schema, full annotations, and 100% schema coverage, the description supplies everything else an agent needs: algorithm identity, sensitivity niche, default subject scope, version pinning, and offline behavior. Nothing material is missing.

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 coverage is 100%, so every parameter is already documented inline (evalue, source, threshold, max_target_seqs, domain_inclusion_evalue). The description only elaborates on subjects' default-vs-FASTA behavior, adding marginal value over 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?

States the specific algorithm (DELTA-BLAST), the operation (build a position-specific profile from SMART domains, then search), and the resource (proteins). It explicitly contrasts with BLASTP ('more sensitive than BLASTP for distant homologs'), letting an agent distinguish it from the nearby blast_search/rps_blast_smart family.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives clear usage context: use it for distant homolog detection where BLASTP would miss, and the default search scope is spelled out ('open record's coding sequences unless subjects gives FASTA'). It does not explicitly name the sibling alternatives to use when sensitivity is not needed, so 4 rather than 5.

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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