cdskit translate

cdskit translate converts CDS nucleotide sequences to amino-acid sequences.

Example

cdskit translate --seq_file cds.fasta --out_file proteins.fasta --codon_table 1

Stop-aware translation

cdskit translate --seq_file cds.fasta --out_file proteins.fasta --to_stop yes

With --to_stop yes, translation stops at the first in-frame stop codon.

Key options

• --codon_table INT: NCBI codon table ID.
• --to_stop yes|no: Stop translation at the first stop codon instead of emitting *.

Notes

• Input sequences must be DNA and their lengths must be multiples of three.
• Gap-only codons translate to -.
• Partial-gap codons and unresolved ambiguous codons translate to X. Ambiguities with one translation remain resolvable, for example GCN is A and TAR is * under the standard code.
• For genetic codes with context-dependent stops (27, 28, and 31), translation uses the amino-acid assignment for dual-use codons because the sequence alone does not identify termination context. --to_stop yes therefore does not stop at a dual-use codon. Backalignment follows the same rule.

Ordinary translation versus an explicitly complete CDS

Ordinary translation uses the forward amino acid for dual-coding codons in codes 27/28/31. --to_stop yes stops only at a definite translated *, including standard-code TAR; it does not infer context-dependent termination. This is an intentional CDSKIT contract; Biopython's direct to_stop=True rejects these code tables instead.

--complete_cds yes explicitly asserts complete CDS boundaries. It requires a valid start codon, length divisible by three, a terminal-compatible stop, and no definite internal stops or missing/invalid codons. The initiator becomes M and the terminator is omitted, regardless of --to_stop. The ordinary default is unchanged. Possible ambiguous internal stops remain X; acceptance is not proof of biological completeness or function.

cdskit translate --seq_file complete_cds.fasta --out_file proteins.fasta \
  --codon_table 27 --complete_cds yes

See codon semantics for uncertainty and compatibility.

X in DNA is treated as any base, like N, consistently in ordinary, partial-tail and complete-CDS translation. Invalid alphabet characters are rejected even when the same codon also contains a missing character.

References

Cite the method or resource actually used and report the CDSKIT version and options.

• Cock PJA et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422–1423. Paper — Sequence parsing, feature extraction and genetic-code infrastructure used by CDSKIT.
• Swart EC, Serra V, Petroni G, Nowacki M (2016). Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination. Cell 166:691–702. Paper — Biological background for context-dependent termination in the discussed ciliate codes; CDSKIT does not infer termination context.