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数据与复现
BI
bio-alignment-msa-parsing
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-alignment-msa-parsing
- 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
- 解析 multiple sequence alignments to extract information，analyze content，、 prepare ，用于 downstream analysis。
- Goal：Load modules ，用于 parsing，analyzing，、 manipulating multiple sequence alignments。
- Approach：Import AlignIO ，用于 reading，Counter ，用于 column analysis，、 alignment classes ，用于 constructing modified alignments。
原始文档
SKILL.md 摘录
Loading Alignments
Goal: Read an MSA file and inspect its dimensions.
Approach: Use AlignIO.read() specifying the file and format.
Column-wise Analysis
Goal: Analyze alignment content column by column to assess composition, conservation, and variability.
Approach: Use column indexing (alignment[:, idx]) and Counter to examine character frequencies at each position.
Gap Analysis
Goal: Quantify gap distribution across sequences and columns to identify problematic regions or sequences.
Approach: Count gap characters per sequence and per column, then identify positions exceeding a gap fraction threshold.
适用场景
- 适合在parsing 或 manipulating multiple sequence alignments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 - Read/write alignment files in various formats
- pairwise-alignment - Create pairwise alignments
- msa-statistics - Calculate conservation metrics
- sequence-manipulation/motif-search - Search for patterns
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