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BioPython MCP Server

BioPython MCP Server

by kmaneesh
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Hybrid

pairwise_align

Align two biological sequences using pairwise alignment. Supports global (Needleman-Wunsch) and local (Smith-Waterman) modes with customizable match, mismatch, and gap penalties to identify sequence similarity.

Instructions

Perform pairwise sequence alignment.

Args: seq1: First sequence seq2: Second sequence mode: Alignment mode - 'global' or 'local' (default: 'global') match_score: Score for matching residues (default: 2.0) mismatch_score: Score for mismatching residues (default: -1.0) gap_open: Gap opening penalty (default: -2.0) gap_extend: Gap extension penalty (default: -0.5)

Returns: Dictionary containing alignment results and statistics

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": {
      "seq1": "<seq1>",
      "seq2": "<seq2>"
    },
    "name": "pairwise_align"
  }
}

Input Schema

NameRequiredDescriptionDefault
seq1Yes
seq2Yes
modeNoglobal
match_scoreNo
mismatch_scoreNo
gap_openNo
gap_extendNo

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.8

TDQS

A3.8/5.0
Behavior3/5

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

With no annotations provided, the description carries the full burden. It lists parameters and return type, but does not disclose behavioral traits such as computational complexity, sequence length limits, or side effects (though none expected). A basic description, but not deeply transparent.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description uses a standard docstring format with parameter listings, which is clear but somewhat verbose—many default values are already in the schema. While not excessively long, it could be more concise by omitting redundant default indicators.

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?

The tool has 7 parameters (2 required) with no schema descriptions, and an output schema exists but is not detailed in the description. The description covers all parameters and states the return type as a dictionary with alignment results, which is adequate for a standard bioinformatics tool.

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?

Given that the input schema has 0% description coverage, the description compensates by naming each parameter (seq1, seq2, mode, match_score, etc.) and explaining their defaults and meaning (e.g., 'Score for matching residues'). This adds value beyond the bare schema.

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 explicitly states 'Perform pairwise sequence alignment' and lists two sequences and mode (global/local), clearly distinguishing it from sibling tools like multiple_sequence_alignment or build_phylogenetic_tree. The verb 'perform' combined with 'pairwise sequence alignment' precisely identifies the function.

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 use when pairwise alignment of two sequences is needed, but it does not provide explicit guidance on when to choose global vs local mode, nor does it mention alternatives like multiple_sequence_alignment. It lacks 'when'/'when not' statements.

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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