BioPython MCP Server

Overview Schema Source Related Servers Discussions Admin

find_motif

Search DNA, RNA, or protein sequences for a motif pattern, returning all positions and count of occurrences, with optional overlapping matches.

Instructions

Find all occurrences of a motif in a sequence.

Args: sequence: DNA, RNA, or protein sequence to search motif: Motif pattern to find overlapping: Allow overlapping matches (default: True)

Returns: Dictionary containing motif positions and count

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "sequence": "<sequence>",
      "motif": "<motif>"
    },
    "name": "find_motif"
  }
}

Input Schema

Name	Required	Description	Default
`sequence`	Yes
`motif`	Yes
`overlapping`	No

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.8Feb 5, 2026

TDQS

A4/5.0

Behavior3/5

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

No annotations exist, so description carries full burden. It explains core behavior (find motif, return positions/count) but lacks details on edge cases, algorithm, or performance.

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?

Description is brief, structured as Args/Returns, and front-loaded. Every sentence is necessary with no redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given low complexity, description covers parameters and return value. Could mention edge cases like empty sequence or motif not found, but overall adequate.

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 coverage is 0%, but description explains all three parameters: sequence, motif, and overlapping (with default). This adds semantic meaning beyond the schema's types.

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 'Find all occurrences of a motif in a sequence' with specific verb and resource. It distinguishes from sibling tools like reverse_complement or translate_sequence.

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?

The description implies usage for finding motifs but does not explicitly state when to use or exclude alternatives like find_active_site or multiple_sequence_alignment.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.