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by com.seqbench

ASO Gapmer Designer

aso_design
Read-onlyIdempotent

Design antisense-oligonucleotide (ASO) gapmers against an mRNA target: scans candidate sites, builds the antisense oligo in the standard 5-10-5 architecture (chemically-modified wings, central DNA gap for RNase H1, phosphorothioate backbone), and screens each for known liabilities (G-quadruplex motifs, CpG immunostimulation, self-complementarity, GC extremes). No transcriptome-wide off-target search.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
wingNoModified-wing length on each side (nt); the central gap = length − 2×wing.
lengthNoTotal gapmer length (nt).
targetYesNucleotide sequence (raw or FASTA; IUPAC accepted).

TDQS

A4.5/5.0
Behavior5/5

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

Beyond the annotations (readOnlyHint, idempotentHint), the description adds rich behavioral context: it scans candidate sites, builds the antisense oligo with specific chemistry, screens for liabilities, and explicitly states what it does not do. This fully informs the agent of the tool's behavior.

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 long, front-loads the core purpose, and includes all essential details without unnecessary words. Every sentence adds value.

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

Completeness3/5

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

While the purpose and behavior are well described, the output format is not mentioned. With no output schema to rely on, the agent is left uncertain about what the tool returns (e.g., list of designs, scores). This gap reduces completeness for a read-only design tool.

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?

The input schema covers all three parameters with descriptions, but the description adds meaningful context by explaining the 5-10-5 architecture linking wing and length, and the screening steps. This provides additional semantics beyond the schema defaults and 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 designs ASO gapmers against mRNA targets, specifies the 5-10-5 architecture, and distinguishes itself from sibling tools like siRNA or CRISPR design tools by focusing on antisense oligonucleotides and explicitly mentioning no transcriptome-wide off-target search.

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 gives clear context for when to use this tool (for ASO gapmer design) and mentions a key limitation (no transcriptome-wide off-target search), implying alternative tools might be needed for that. However, it does not explicitly name alternatives or state 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.

Resources