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bio-alignment-pairwise
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-alignment-pairwise
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- Python：PairwiseAligner() (BioPython Bio.Align)。
- CLI：needle (global) 或 water (local) ，面向 EMBOSS。
- R：pairwiseAlignment() (Biostrings)。
- Align two sequences" → Compute optimal alignment between pair of sequences ，使用 dynamic programming. Python：PairwiseAligner() (BioPython Bio.Align) CLI：needle (global) 或 water (local) ，面向 EMBOSS R：pairwiseAlignment() (Biostrings)。
- Align two sequences ，使用 dynamic programming algorithms (Needleman-Wunsch ，用于 global，Smith-Waterman ，用于 local)。
原始文档
SKILL.md 摘录
Required Import
Goal: Load modules needed for pairwise alignment operations.
Approach: Import the PairwiseAligner class along with sequence and I/O utilities from Biopython.
Core Concepts
| Mode | Algorithm | Use Case |
|---|---|---|
global | Needleman-Wunsch | Full-length alignment, similar-length sequences |
local | Smith-Waterman | Find best matching regions, different-length sequences |
Creating an Aligner
Goal: Configure a PairwiseAligner with appropriate scoring for the sequence type.
Approach: Instantiate PairwiseAligner with mode, scoring parameters, or a substitution matrix depending on DNA vs protein input.
适用场景
- 适合在comparing two sequences，finding optimal alignments，scoring similarity，、 identifying local 或 global matches between DNA，RNA，或 protein sequences时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- alignment-io - Save alignments to files in various formats
- msa-parsing - Work with multiple sequence alignments
- msa-statistics - Calculate identity, similarity metrics
- sequence-manipulation/motif-search - Pattern matching in sequences
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