bio-alignment-pairwise
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill pairwise-alignment --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+ 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 `Bio.Align.PairwiseAligner` is the right default for interactive use, scripting, and pair
- Version Compatibility
- Required Import
- Pairwise Library Selection
- Core Concepts
- Choosing the Right Mode
- DNA vs Protein Alignment
- Creating an Aligner
- Performing Alignments
- Alignment Output Format
- Accessing Alignment Data
- Alignment Counts (Identities, Mismatches, Gaps)
- Common Scoring Configurations
- PairwiseAligner Default Gap Penalties Are 0
- DNA/RNA Alignment
What does the bio-alignment-pairwise skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill pairwise-alignment --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.