find_orfsFind open reading frames (ATG…stop) across all six frames.
| Name | Required | Description | Default |
|---|---|---|---|
| sequence | Yes | Nucleotide sequence (raw or FASTA; IUPAC accepted). | |
| minAaLength | No | Minimum protein length (aa) to report. | |
| requireStop | No | Only report ORFs terminated by a stop codon. |
Changes observed during successful MCP inspections. Dates show when Glama detected each change.
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint=true and idempotentHint=true. Description adds minimal extra behavior disclosure beyond 'across all six frames'. No contradictions, but limited added value.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Single sentence, perfectly concise, and front-loaded with the action. No unnecessary words.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given 3 well-documented parameters and no output schema, the description sufficiently states the core function. Could mention output format but not essential for basic use.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, so baseline is 3. Description does not add meaning beyond schema; it does not elaborate on parameters like minAaLength or requireStop.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description uses specific verb 'Find' and resource 'open reading frames (ATG…stop)' with scope 'across all six frames'. This clearly distinguishes it from sibling tools like translate or motif_finder.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies usage for ORF detection but lacks explicit guidance on when not to use or alternatives (e.g., translate for simple translation). No exclusions or context provided.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Add one secure layer between your agents and this server.
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.
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'.
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.
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.