---

name: sequence-objects-and-features description: "Operate Biopython Seq, MutableSeq, SeqRecord, SeqFeature, location, codon-table, and SeqUtils workflows without file parsing." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

sequence-objects-and-features

Use this sub-skill when the task is about in-memory Biopython sequence objects, record annotations, feature locations, translation/transcription/reverse-complement logic, codon tables, or Bio.SeqUtils helpers.

Route here

• Build or transform Seq, MutableSeq, or SeqRecord objects from already-available sequence strings or records.
• Add, inspect, slice, extract, shift, or reverse-complement SeqFeature, SimpleLocation, CompoundLocation, and fuzzy positions.
• Diagnose translation behavior for complete CDS features, codon_start, transl_table, start/stop codon checks, and ambiguous codons.
• Work with SeqRecord.annotations, dbxrefs, features, and length-checked letter_annotations.
• Use safe sequence utilities such as gc_fraction, molecular_weight, nt_search, seq1, seq3, GC_skew, and CodonAdaptationIndex.

Route elsewhere

• Sequence/alignment/search file parsing, writing, indexing, or format conversion: use file-io-and-format-conversion.
• Pairwise/multiple alignments, BLAST/SearchIO result models, and phylogenetic trees: use alignment-search-and-phylogeny.
• PDB/mmCIF structures, SMCRA traversal, polypeptide extraction from structures, and structural superposition: use structural-bioinformatics.
• Online database retrieval, Entrez/KEGG web access, and BioSQL storage: use web-databases-and-biosql.

Operating procedure

1. Identify the object level: raw string, Seq/MutableSeq, SeqRecord, SeqFeature, or Location.
2. Keep coordinates explicit: Biopython feature coordinates are Python-style zero-based, half-open intervals; reverse-strand locations still use left/right genomic boundaries.
3. Preserve annotation intentionally: slicing, concatenation, translation, and reverse-complementing do not preserve every field by default.
4. For CDS translation, inspect the genetic table, codon_start, length modulo three, start codon, terminal stop codon, and internal stops before changing code.
5. For non-trivial behavior or environment checks, run scripts/sequence_feature_smoke.py; it uses only in-memory data and should print PASS.

Bundled references

• references/sequence-feature-api.md — verified API signatures, object relationships, coordinate rules, feature extraction recipes, and SeqUtils notes.
• references/troubleshooting.md — failure diagnosis for annotations, locations, reverse complements, CDS translation, and utilities.