Jean — Molecular Biology & Genomics

blast_project_sequences

Read-only

Search a sequence against THIS PROJECT'S OWN records with blastn or blastp, on this machine: the local database is built from every project record of the program's alphabet, and every E-value is computed from that database's own size.

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.
`region`	No	which part of the open record to search, when no sequence is wired in. Values: whole (the whole record), selection (the current selection), feature (a named feature).	whole
`feature`	No	the feature's name, matched case-insensitively on the open record. Only applies when region is feature.
`program`	No	blastn searches the nucleotide records, blastp the protein records. Values: blastn (blastn · nucleotide query), blastp (blastp · protein query).	blastn
`_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 query. Wire a record or a sequence output, or paste raw/FASTA. Left empty, the region below is taken from the open record.
`maxExpect`	No	E-value cutoff (BLAST+'s -evalue); hits above it are not reported.

Output Schema

Name	Required	Description
`hits`	Yes	every hit, with its HSPs, accession, organism and the links the service sent
`topHit`	Yes	the best hit by E-value: what a "what is this?" step reads
`tabular`	Yes	the hits as BLAST's own outfmt 6 table, for download or a downstream parser
`hitCount`	Yes	how many subjects matched
`sequences`	Yes	the hit subjects as FASTA, ready to wire straight into an alignment or a tree
`topExpect`	Yes	the best hit's E-value; wire into a $when to branch on significance
`provenance`	Yes	the binary, the command line EBI ran, the databases as built, and the search space the E-values are relative to
`topCoverage`	Yes	what fraction of the query the best hit covers, 0–1
`topIdentity`	Yes	percent identity of the best hit's best HSP

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedOct 25, 2026
- addedOutput schema / properties / topIdentity / x-unit
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Added value: +"%"
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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 declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is covered. Beyond that, the description adds genuinely useful behavior: the database is built from every project record of the program's alphabet, and E-values are computed against that database's own size — a non-obvious statistical detail an agent could not get from the schema. It does not discuss runtime, DB build cost, or result size, keeping it short of a 5.

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 sentence, front-loaded with the core action and scope, with no filler sentences. Some phrasing is redundant ('on this machine' after 'local database') but the dense construction is efficient overall.

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?

For a read-only local BLAST with a fully documented schema and an output schema, the description covers purpose, scope and the E-value basis adequately. Minor gaps remain: what happens when sequence is omitted (region fallback), and any constraint that the project must contain records of the chosen alphabet, though the schema hints at the former.

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 all seven parameters including the nested _subject and _files objects are already documented in the schema; baseline is 3. The description reinforces program choice (blastn vs blastp tied to the database's alphabet) and the E-value basis, but adds no format or wiring detail beyond what the schema states.

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?

States a specific verb and resource (search a sequence against the project's own records with blastn/blastp) and emphasizes the local, project-scoped database, which separates it from the remote-DB siblings such as blast_search or the rps_blast family. It never names an alternative tool explicitly, so the differentiation is implied by the 'THIS PROJECT'S OWN' framing rather than spelled out.

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 usage context — local project-wide search rather than a remote database search — via 'on this machine' and 'every project record'. However there is no explicit when-to-use/when-not clause and no named alternative, so an agent must infer that blast_search is the right tool for external databases.

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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