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.
Profile →npx skills add majiayu000/claude-skill-registry --skill pairwise-alignment-gptomics-bioskills-3e39e6e4 --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.
# Pairwise Sequence Alignment Align two sequences using dynamic programming algorithms (Needleman-Wunsch for global, Smith-Waterman for local). ## Required Import ```python from Bio.Align import PairwiseAligner from Bio.Seq import Seq from Bio import SeqIO ``` ## Core Concepts | Mode | Algorithm | Use Case | |------|-----------|----------| | `global` | Needleman-Wunsch | Full-length alignment, similar-length sequences | | `local` | Smith-Waterman | Find best matching regions, different-length sequences | ## Creating an Aligner ```python # Basic aligner with defaults aligner = PairwiseAligner() # Configure mode and scoring aligner = PairwiseAligner(mode='global', match_score=2, mismatch_score=-1, open_gap_score=-10, extend_gap_score=-0.5) # For protein alignment with substitution matrix from Bio.Align import substitution_matrices aligner = PairwiseAligner(mode='global', substitution_matrix=substitution_matrices.load('BLOSUM62')) ``` ## Performing Alignments ```python seq1 = Seq('ACCGGTAACGTAG') seq2 = Seq('ACCGTTAACGAAG') # Get all optimal alignments alignments = aligner.align(seq1, seq2) print(f'Found {len(alignments)} optimal alignments') print(alignments[0]) # Print first alignme
- Required Import
- Core Concepts
- Creating an Aligner
- Performing Alignments
- Alignment Output Format
- Accessing Alignment Data
- Alignment Counts (Identities, Mismatches, Gaps)
- Common Scoring Configurations
- DNA/RNA Alignment
- Protein Alignment
- Local Alignment (Find Best Region)
- Semiglobal (Overlap/Extension)
- Available Substitution Matrices
- Working with SeqRecord Objects
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 majiayu000/claude-skill-registry --skill pairwise-alignment-gptomics-bioskills-3e39e6e4 --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 majiayu000/claude-skill-registry, a repository with 534 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.