genpark-smith-waterman-local-sequence-aligner-skill

Smith-Waterman dynamic programming algorithm finding exact optimal local alignment motifs, homologous domains, and substrings across DNA and protein sequences.

Architecture Overview

flowchart TD
    A[Agentic AI / Bioinformatics Orchestrator] -->|FASTA / DNA / Tree Matrix| B[MCP Server / Client]
    B --> C[genpark-smith-waterman-local-sequence-aligner-skill Bio-Kernel]
    C --> D[Dynamic Programming / Hierarchical Tree / BWT Index]
    D --> E[Exact Alignment & Evolutionary Output]
    E -->|Structured Payload| A

Loading

Features

• 0 External Pip Dependencies: Pure Python standard library implementation.
• MCP Protocol Ready: Includes Model Context Protocol server script (mcp_server.py).
• Production Standard: Comprehensive biochemical test cases, ultra-fast DP matrices.

Quick Start

python example_usage.py