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Glama

Sequence Format Converter

sequence_format_convert
Read-onlyIdempotent

Convert between FASTA and GenBank (whole sequence, CDS or protein), or export to TSV.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
toNoOutput format. fasta-cds / fasta-protein extract CDS features (GenBank input only). GenBank in and 'genbank' out rewrites the record with its features, qualifiers and topology intact — it is a rewrite, not a re-annotation.fasta
fromNoInput format; 'auto' sniffs it from the first meaningful line.auto
inputYesA FASTA or GenBank record to convert.

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Changed1 schema field changed
    • changedInput schema / properties / to / description
      Previous value: -"Output format. fasta-cds / fasta-protein extract CDS features (GenBank input only)."New value: +"Output format. fasta-cds / fasta-protein extract CDS features (GenBank input only). GenBank in and 'genbank' out rewrites the record with its features, qualifiers and topology intact — it is a rewrite, not a re-annotation."
  2. First observed

TDQS

A3.5/5.0
Behavior3/5

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

Annotations already provide readOnlyHint and idempotentHint, so the safety profile is covered. The description adds no additional behavioral context, such as how 'genbank' output preserves features or that CDS extraction is GenBank-only—that detail lives in the schema parameter description instead. There is no contradiction with annotations, but the description itself contributes little beyond what structured fields already state.

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 efficient sentence that leads with the core function and its options. There is no fluff, no repetition of schema details, and it is appropriately short for a simple conversion tool. Every word earns its place.

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?

For a tool with three parameters and no output schema, the description is adequate but leaves some gaps. It does not mention the return format (e.g., a string or file), error handling for invalid input, or how multiple records are treated. Given the simplicity and the strong schema coverage, this is sufficient for basic use, but an agent might need to infer expected output shape from tool naming conventions.

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 description coverage is 100%, with detailed parameter descriptions for 'to' and 'from' already present, including the rewrite-vs-reannotation nuance. The tool description does not add any parameter-specific meaning beyond what the schema provides. The baseline of 3 applies because the schema does the heavy lifting.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the action by naming the formats involved (FASTA, GenBank, TSV) and the specific options (whole sequence, CDS, protein). However, it does not explicitly distinguish itself from siblings like format_sequence or parse_genbank, which likely have overlapping purposes. The verb 'Convert' is specific, but the lack of sibling differentiation keeps it from a 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Usage is implied—it converts between formats—but there is no explicit guidance on when to choose this tool over alternatives such as format_sequence or parse_genbank. No when-not or exclusion conditions are given. The description relies on the user to infer that this is the go-to for format conversion.

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