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by com.seqbench

HDR donor designer

crispr_hdr_donor
Read-onlyIdempotent

Build an HDR donor (homology arms flanking an edit) from a target sequence and either an explicit edit window (editStart/editEnd) or a guide's cut site (guideStart/guideEnd/guideStrand/nuclease — SpCas9-family only; Cas12a's staggered cut needs an explicit editStart/editEnd). Also designs genotyping primers spanning the edit site on the original sequence (a real size-shift or sequencing target to confirm the edit), reusing the same primer-design engine as primer_design.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
editEndNo1-based inclusive end of the region being replaced; editEnd = editStart-1 denotes a pure insertion with nothing removed. Omit to derive from the guide's cut site.
blockPamNoWhen a SpCas9-family guide is supplied and the edit does not already disrupt its PAM, fold a PAM-blocking mutation (silent when a CDS frame is given) into the donor so the edited allele can't be re-cut.
guideEndNo1-based forward-strand end of the guide's protospacer.
nucleaseNoNeeded only when deriving the cut site from guideStart/guideEnd/guideStrand.spcas9
armLengthNoHomology arm length (bp) on each side. Use ~30–60 for an ssODN donor, ~500–1000 for a dsDNA donor plasmid.
editStartNo1-based start of the region being replaced. Omit to derive from guideStart/guideEnd/guideStrand instead.
frameStartNoOptional 1-based CDS reading-frame start; makes the PAM-blocking mutation synonymous where possible.
guideStartNo1-based forward-strand start of the guide's protospacer (alternative to editStart/editEnd, for an insertion exactly at the cut site).
guideStrandNoStrand the guide's protospacer is on.
replacementYesSequence to insert/substitute ("" for a pure deletion).
targetSequenceYesNucleotide sequence (raw or FASTA; IUPAC accepted).
designGenotypingPrimersNoAlso design a primer pair (on the original targetSequence) whose product spans the edit site.

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and idempotentHint=true, establishing safety. The description adds meaningful context: it reuses primer_design engine, auto-designs genotyping primers, and handles PAM disruption. No contradictions with annotations. Additional detail about 'real size-shift or sequencing target' adds transparency.

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 a single paragraph of about 4 sentences, front-loaded with the core purpose. Every sentence contributes necessary information without redundancy. It efficiently covers modes, nuclease constraints, and secondary functionality (genotyping primers).

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?

The description explains inputs and high-level outputs but does not specify the exact return format (e.g., what sequences or primer pairs are returned). Since there is no output schema, this information is needed for the agent to understand how to use the result. Otherwise, it covers the main use cases and parameter interactions.

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 100%, so baseline is 3. The description adds value beyond the schema by grouping parameters into two modes (edit window vs guide cut) and explaining edge cases like Cas12a requiring explicit edit window. It also clarifies the purpose of blockPam and frameStart in the context of PAM disruption.

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 builds an HDR donor with homology arms flanking an edit. It specifies two modes: explicit edit window or guide cut site, and mentions it designs genotyping primers. It distinguishes from sibling tools like primer_design by noting it reuses its engine, and covers nuclease-specific constraints (Cas12a needs explicit window). No ambiguity.

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 clear guidance on when to use explicit editStart/editEnd versus guide parameters, especially for Cas12a. It also explains PAM-blocking behavior. However, it does not explicitly compare to other design tools like prime_editing_design or base_editing_design, leaving the decision to the agent's broader context.

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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