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by com.seqbench

HGVS Variant Converter (c. <-> g. <-> p.)

hgvs_convert
Read-onlyIdempotent

Parse an HGVS "c." variant description (by gene symbol, RefSeq NM_, or Ensembl ENST accession), convert it to genomic (g.) coordinates via a real, live-fetched Ensembl exon/CDS map (transcripts resolved through the bundled MANE RefSeq<->Ensembl crosswalk), apply 3'-rule normalization to any del/dup/ins, and predict the protein (p.) effect where that is safely computable. Refuses cleanly — rather than guessing — for circular/mitochondrial genomes, RNA-level or protein-level input, uncertain/mosaic syntax, splice-junction-adjacent or inversion protein effects, and non-MANE/non-Ensembl transcripts.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
variantYesA full HGVS "c." variant description: "<accession or gene symbol>:c.<edit>", e.g. "NM_000546.6:c.215C>G" or "TP53:c.215C>G". Substitution (">"), deletion ("del"), duplication ("dup"), insertion ("ins"), delins, and inversion ("inv") are supported.

TDQS

A4.9/5.0
Behavior5/5

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

Beyond annotations (readOnlyHint, idempotentHint), the description details internal processes (live Ensembl maps, MANE crosswalk, 3'-rule normalization) and refusal reasons, adding significant behavioral context. No contradiction with annotations.

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?

Every sentence is informative and earns its place. The description is well-structured with a clear purpose, detailed behavior, and explicit limitations, all without unnecessary verbosity.

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?

Given the tool's complexity and high parameter documentation, the description covers most aspects. However, it lacks explicit mention of the output structure (e.g., what fields are returned), which would enhance completeness for an output-schema-less tool.

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

Parameters5/5

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

The sole parameter 'variant' has full schema coverage, but the description adds crucial context: required format with examples, supported accessions and edit types, which goes beyond the schema definition.

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 it converts HGVS 'c.' descriptions to genomic coordinates and predicts protein effects. It specifies supported accessions (gene symbol, RefSeq, Ensembl) and edit types, distinguishing it from sibling tools like variant_annotate.

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

Usage Guidelines5/5

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

The description explicitly states when to use the tool and lists clear refusal cases (circular/mitochondrial genomes, RNA/protein input, uncertain syntax, etc.), providing excellent guidance on when not to use it.

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.

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