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Data & Repro
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FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-alignment-msa-parsing
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-alignment-msa-parsing
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Parse multiple sequence alignments to extract information, analyze content, and prepare for downstream analysis.
- Goal: Load modules for parsing, analyzing, and manipulating multiple sequence alignments.
- Approach: Import AlignIO for reading, Counter for column analysis, and alignment classes for constructing modified alignments.
Source Doc
Excerpt From SKILL.md
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.
Use cases
- Use when parsing or manipulating multiple sequence alignments.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- 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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