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name: sequence-analysis description: "Use Biotite for sequence construction, alphabets, annotations, translation, pairwise and multiple alignment, k-mer searches, profiles, phylogenetic trees, and sequence-centered graphics." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

Sequence Analysis

Use this sub-skill when a task is centered on biotite.sequence, biotite.sequence.align, biotite.sequence.phylo, or sequence-centered biotite.sequence.graphics workflows.

Route Here For

• Constructing NucleotideSequence, ProteinSequence, GeneralSequence, custom Alphabet/LetterAlphabet, and PositionalSequence objects.
• Validating symbols, choosing ambiguous vs unambiguous nucleotide alphabets, slicing/editing sequences, concatenating sequences, and reading .code/.symbols safely.
• Translating nucleotide sequences, finding ORFs, using CodonTable, reverse complements, and protein letter conversions.
• Building Feature, Location, Annotation, and AnnotatedSequence objects and slicing annotations or extracting feature sequences.
• Pairwise alignment with align.align_optimal(), align.align_ungapped(), align.align_banded(), local/gapped/ungapped seed extension, and alignment scoring/identity.
• Multiple sequence alignment with align.align_multiple(), guide trees, k-mer based prefiltering, profiles, consensus sequences, and position-specific scoring matrices.
• Creating or parsing phylo.Tree/TreeNode objects, UPGMA/neighbor-joining trees, Newick strings, and sequence dendrogram plots.
• Deciding when sequence graphics such as alignment plots, sequence logos, feature maps, plasmid maps, and dendrograms need optional matplotlib.

Use Another Biotite Sub-skill For

• FASTA, FASTQ, GenBank, GFF, Clustal, parser classes, and format round trips: ../file-io-formats/SKILL.md.
• Entrez, UniProt, RCSB, PubChem, AlphaFold DB, BLAST, MSA application wrappers, and network/external binary planning: ../database-application/SKILL.md.
• PyMOL, RDKit, OpenMM, display backends, and visualization/export tasks where sequence data is not the main object: ../interfaces-visualization/SKILL.md.

Start With

1. Choose the concrete sequence type and alphabet before building downstream objects.
2. For alignments, choose the substitution matrix, gap model, local vs global semantics, and whether max_number should cap equally optimal traces.
3. For annotations, keep track of 1-based biological feature positions vs Python sequence slicing positions.
4. For profiles/MSAs/trees, ensure every input sequence is already comparable and that alignment/profile shapes match.

References

• API map: references/api-reference.md.
• Task recipes: references/workflows.md.
• Failure recovery: references/troubleshooting.md.
• Safe local check: scripts/sequence_alignment_smoke.py.

Quick Smoke Check

Run this helper when you need to verify the local Biotite sequence surface without network or source checkout access:

python sub-skills/sequence-analysis/scripts/sequence_alignment_smoke.py --mode all

The helper uses tiny literal sequences, exits nonzero on failed assertions, and can run only selected checks with --mode core, --mode alignment, or --mode profile.