bio-alignment-pairwise skillA
bio-alignment-pairwise is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
## Version Compatibility Reference examples tested with: BioPython 1.83+ 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. # Pairwise Sequence Alignment **"Align two sequences"** -> Compute an optimal alignment between a pair of sequences using dynamic programming. - Python: `PairwiseAligner()` (BioPython Bio.Align) - CLI: `needle` (global) or `water` (local) from EMBOSS - R: `pairwiseAlignment()` (Biostrings) Align two sequences using dynamic programming algorithms (Needleman-Wunsch for global, Smith-Waterman for local). ## Required Import **Goal:** Load modules needed for pairwise alignment operations. **Approach:** Import the PairwiseAligner class along with sequence and I/O utilities from Biopython. ```python from Bio.Align import PairwiseAligner from Bio.Seq import Seq from Bio import SeqIO ``` ## Pairwise Library Selection …
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How to install
mdr add pku-yuangroup/openai4s/bio-alignment-pairwise@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-alignment-pairwise@sha256:84bcd1577bf10987Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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