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Search the parts library

parts_library_search
Read-onlyIdempotent

Search a parts list harvested from the annotated features of the vector library — promoters, terminators, RBSs, polyA signals, origins, selection markers, affinity tags, reporters, linkers/MCSs — by name, kind or length. Nothing here is transcribed: every part is the exact sequence a GenBank record annotated, and each hit carries the accession and 1-based span it was cut from, plus every other library vector the same part was found in. Parts whose location is spliced or approximate are excluded, because their sequence is not fully determined.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
kindsNoRestrict to these part kinds (promoter, terminator, origin, RBS, polyA, selection marker, affinity tag, reporter, linker/MCS, …). An unknown kind is an error.
limitNoMaximum hits to return. Capped at 100; asking for more is an error, not a silent truncation.
queryNoSubstring of the part name (min 2 characters), e.g. "T7", "AmpR", "SV40 polyA".
maxLengthNoLargest part length in bp.
minLengthNoSmallest part length in bp.
includeSequenceNoInclude each part's bases (5'→3' on the part's own strand).

TDQS

A4.5/5.0
Behavior5/5

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

Annotations already mark readOnlyHint, idempotentHint, and openWorldHint false, but the description adds substantial behavioral detail beyond this: nothing is transcribed, each hit carries the accession and 1-based span it was cut from, hit parts may appear in multiple library vectors, and spliced or approximate parts are excluded because their sequence is not fully determined. This gives the agent insight into both the return payload and the filtering boundary.

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?

The description is packed with relevant information and every clause earns its place. It front-loads the main purpose and the precise data source, then clarifies boundary behavior in a single final sentence. Despite its richness, it remains a single readable paragraph without redundancy.

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?

For a search tool with six optional parameters and no output schema, the description covers the essential execution expectations: what kinds of parts are searchable, how exact sequences are handled, what result metadata appears, and which parts are excluded. Combined with the annotations and fully self-documenting input schema, an agent has enough context to decide to invoke the tool and how to interpret its results.

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 six parameters, including constraints on limit and kinds, are already documented in the schema. The description contributes lexical context (promoters, terminators, RBSs, polyA signals, etc.) but does not add meaning beyond what the parameter descriptions already provide. Baseline 3 is appropriate for this level of schema coverage.

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 a specific verb ('search'), a well-defined resource ('a parts list harvested from the annotated features of the vector library'), and the searchable dimensions (name, kind, length). The description also highlights a defining scope: parts are the exact sequences from GenBank annotations, while spliced or approximate locations are excluded. This sharply distinguishes the tool from generic sequence search or whole-vector search siblings.

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?

The description clearly indicates when the tool applies: searching for defined genetic parts from vector parts libraries, with filtering by name, kind, or length. It does not explicitly name a sibling alternative or state 'when not to use this,' but the context and content make the appropriate scenario obvious. A small deduction because alternatives like vector_library_search are not explicitly contrasted.

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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TDQS

A3.6/5.0
Disambiguation4/5

Most tools have highly specific purposes (e.g., crispr_grna_design vs base_editing_design vs prime_editing_design). However, there is some overlap in sequence analysis tools (characterize_sequence, sequence_report) and plasmid annotation tools (plasmid_annotate vs plasmid_deep_annotate) which could cause confusion.

Naming Consistency3/5

The naming pattern is largely consistent with snake_case verb_noun or noun_descriptor (e.g., primer_design, plasmid_annotate, fastq_trim). However, there are exceptions like 'batch', 'workflow', 'gc_content', and 'cloning_diagnose' which don't follow the verb_noun pattern consistently. Also, some names are phrases like 'golden_gate_from_parts'.

Tool Count2/5

With 101 tools, this server is extremely large and likely overwhelming for agents. Even for a comprehensive bioinformatics toolkit, this exceeds a manageable scope, risking agent confusion and inefficient tool selection. A more modular approach would be advisable.

Completeness4/5

The tool surface covers a wide range of bioinformatics workflows including sequence analysis, primer design, cloning, CRISPR, NGS, expression analysis, and data export. There are minor gaps such as lack of a dedicated protein structure prediction tool and limited off-target genome coverage, but overall the set is impressively complete for its domain.

Resources