---

name: sequences-alignment description: "Construct, transform, compare, and align scikit-bio biological sequences and TabularMSA objects." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

scikit-bio Sequences and Alignment

Use this sub-skill when a task involves constructing Sequence, DNA, RNA, or Protein objects; preserving or slicing sequence metadata; transforming nucleotides; translating with GeneticCode; scoring substitutions; creating or indexing TabularMSA; computing alignment scores/distances; or aligning two sequences with scikit-bio.

Route Here For

• Creating DNA, RNA, Protein, or generic Sequence instances with metadata, positional metadata, interval metadata, lowercase handling, or validation choices.
• Inspecting grammar state such as gaps, degenerates, definites, wildcard characters, or alphabets, and using degap, complement, transcription, reverse transcription, or translation workflows.
• Running pairwise alignment with pair_align, pair_align_nucl, or pair_align_prot, then converting PairAlignPath results to aligned strings or TabularMSA.
• Building TabularMSA objects, indexing rows/columns, deriving consensus/conservation summaries, converting to or from AlignPath, and computing align_score or align_dists.
• Troubleshooting invalid characters, lowercase/validation behavior, metadata length mismatches, translation stop handling, substitution/gap scoring, or MSA shape/index errors.

Start With

• references/api-reference.md for concrete signatures, defaults, and object roles.
• references/workflows.md for copy-ready recipes covering construction, transformation, alignment, MSA, scoring, and distance workflows.
• references/troubleshooting.md for diagnosis tables and repair patterns.
• scripts/sequence_alignment_smoke.py for a small deterministic API smoke check that prints JSON.

Boundaries

• For file-format reading/writing, FASTA parsing, metadata serialization, or I/O registry details, use ../io-metadata/SKILL.md and return here after sequences or TabularMSA objects exist.
• For tree construction or phylogenetic interpretation of alignment-derived distances, use ../trees-phylogeny/SKILL.md.
• For distance-matrix statistics, ordination, PERMANOVA, or downstream statistical tests, use ../statistics-ordination/SKILL.md.
• Treat deprecated global_pairwise_align* and local_pairwise_align* wrappers as legacy/educational APIs only; prefer pair_align, pair_align_nucl, and pair_align_prot.

Quick Sanity Check

From this sub-skill directory with scikit-bio installed, run:

python scripts/sequence_alignment_smoke.py

The script itself is safe to execute from arbitrary working directories when addressed by its file path. It imports only public skbio APIs, constructs sequence objects, aligns short DNA sequences, builds a TabularMSA, and prints a compact JSON summary.