bio-alignment-msa-parsing
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill msa-parsing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+, numpy 1.26+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # MSA Parsing and Analysis Parse multiple sequence alignments to extract information, analyze content, and prepare for downstream analysis. ## Required Import **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. ```python from Bio import AlignIO from Bio.Align import MultipleSeqAlignment from Bio.SeqRecord import SeqRecord from Bio.Seq import Seq from collections import Counter import numpy as np import pandas as pd ``` Optional for streaming and Easel-based weighting: ```python import pyhmmer ``` ## Loading Alignments **Goal:** Read an MSA file and inspect its dimensions. **Approach:** Use `AlignIO.read()` specify
- Version Compatibility
- Required Import
- Loading Alignments
- Extracting Sequence Information
- Get All Sequence IDs
- Get Sequences as Strings
- Get Sequence by ID
- Access Descriptions and Annotations
- Column-wise Analysis
- Get Single Column
- Iterate and Count Columns
- Find Conserved Positions
- Gap Analysis
- Count Gaps Per Sequence
What does the bio-alignment-msa-parsing skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill msa-parsing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.