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CRISPR gRNA designer

crispr_grna_design
Read-onlyIdempotent

Find and score candidate guide RNAs (protospacer + PAM) in a target DNA for common nucleases (SpCas9, SpCas9-NG, SaCas9, Cas12a). PREDICTED, NOT MEASURED. No held-out skill statistic is claimed. Both are pre-2016 models superseded in accuracy by Rule Set 2 / Azimuth and by DeepSpCas9, neither of which is shipped here. Treat the ordering as a ranking aid, not an efficiency prediction. Valid for: SpCas9 with an NGG PAM and a 20 nt spacer, and only when enough genomic flanking context is present to build the model's 30-mer / 35-mer window — both scores are null rather than padded otherwise. Nothing is predicted for SaCas9, Cas12a or SpCas9-NG.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
minScoreNoOnly return guides with a heuristic score at least this high (0–100).
nucleaseNoNuclease id. Omit to just list the available nucleases (no scan is performed).spcas9
sequenceYesNucleotide sequence (raw or FASTA; IUPAC accepted).
searchReverseStrandNoAlso scan the reverse strand for guides.

TDQS

A4.4/5.0
Behavior5/5

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

Annotations already mark the tool as readOnlyHint=true and idempotentHint=true. The description goes well beyond by stating that scores are predicted, not measured; that models are pre-2016 and superseded; that ordering is a ranking aid only; and that scores are null rather than padded for invalid conditions (SaCas9, Cas12a, SpCas9-NG). This fully discloses the tool's limitations and behavior, adding significant transparency.

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?

The description is front-loaded with the main purpose in the first sentence. Every subsequent sentence adds value (caveats, validity conditions). While it could be slightly more concise by merging some warnings, the trade-off for clarity is acceptable. No superfluous text.

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?

Despite lacking an output schema, the description explains what the output contains (scored guides), when scores are null, and what the order means. It also handles edge cases (no scan if nuclease omitted). For a tool of this complexity (multiple nucleases, scoring models, validity conditions), the description is remarkably complete without needing to reference external documentation.

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 coverage is 100% — all four parameters have descriptions in the JSON schema. The description does not add new parameter-specific details beyond what the schema already provides (e.g., minScore default, nuclease enum, sequence format, searchReverseStrand). According to guidelines, with high schema coverage the baseline is 3, and the description does not improve upon this.

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 explicitly states the tool finds and scores candidate guide RNAs for specific nucleases, which clearly distinguishes it from siblings like crispr_offtarget_check, prime_editing_design, and others. The verb 'Find and score' paired with 'candidate guide RNAs' makes the action and resource unambiguous, and the listed nuclease names differentiate from related CRISPR tools.

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 strong usage context: it warns that predictions are not measured, models are superseded, and ordering is only a ranking aid. It also specifies validity conditions (only SpCas9 with NGG PAM and sufficient flanking context; null scores otherwise). However, it does not explicitly name alternative tools (e.g., more accurate models) or say when to prefer those, leaving the agent to infer from the caveats.

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