parse_genbankParse a GenBank flat file into its locus, definition, features and sequence.
| Name | Required | Description | Default |
|---|---|---|---|
| text | Yes | A GenBank flat file (LOCUS … FEATURES … ORIGIN … //). |
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 provide readOnlyHint and idempotentHint. The description adds value by specifying that the tool extracts locus, definition, features, and sequence, which is not obvious from annotations alone. However, it does not disclose error handling, input validation requirements, or output format details.
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?
The description is a single, well-structured sentence of 12 words. It front-loads the verb and outcome without any redundant or unnecessary information, earning every word.
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?
For a simple parser with one parameter and no output schema, the description is fairly complete. It explains what the tool does and what data is extracted. Minor gap: it does not describe the return format (e.g., JSON object structure), but overall adequate given the tool's simplicity.
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 coverage is 100% and the parameter description already mentions the GenBank flat file format. The tool description reinforces this but does not add new meaning beyond what the schema provides, so a baseline score of 3 is appropriate.
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 clearly states the action (parse), the specific resource (GenBank flat file), and the output components (locus, definition, features, sequence). It distinguishes itself from sibling tools like 'characterize_sequence' or 'plasmid_annotate' by its unique purpose.
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 provides no guidance on when to use this tool versus alternatives, no mention of prerequisites or when not to use it. The agent must infer usage solely from the tool's name and sibling context, which is insufficient.
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.