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workbench

by com.seqbench

Search sequence databases by name

sequence_search
Read-onlyIdempotent

Resolve a gene/organism name — or a raw NCBI search term — to candidate accessions, instead of guessing one. Returns up to maxResults hits (accession, title, organism); pass the accession you want to sequence_fetch.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
dbNonucleotide
geneNoGene symbol/name, e.g. "BRCA1". Combined with organism (if given) into a search term.
termNoRaw NCBI search term (advanced) — overrides gene/organism when given, e.g. "BRCA1[gene] AND Homo sapiens[orgn]".
organismNoOrganism name, e.g. "Homo sapiens". Optional; narrows the gene search.
maxResultsNoUp to 20.

TDQS

A4.4/5.0
Behavior4/5

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

Annotations indicate readOnlyHint and idempotentHint, and the description adds behavioral context: returns up to maxResults hits with specific fields (accession, title, organism) and that the term parameter overrides gene/organism. No contradictions.

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 two sentences, front-loaded with the core purpose and followed by actionable return details and workflow. Every sentence earns its place with no redundancy.

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?

The description covers the return format and parameter interaction adequately. Without an output schema, it provides enough information for an agent to understand what to expect. It could mention the specific databases but is sufficient.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 80%, and the description adds the key semantic that 'term' overrides 'gene' and 'organism', which is not fully captured in the schema. This adds useful meaning beyond the schema's parameter descriptions.

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?

The description clearly states the tool's purpose: resolving a gene/organism name or raw NCBI search term to candidate accessions, and distinguishes it from sequence_fetch by instructing to pass the resulting accession to that sibling tool.

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 provides explicit usage guidance: use this tool instead of guessing an accession, and then pass the accession to sequence_fetch. It contrasts with the sibling tool sequence_fetch, but does not explicitly exclude other siblings.

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