Source: https://guthlabs.ai/docs/instruments/codon-dna-rna-protein-translator/mechanism/

instrument mechanism / verified-clean

# Codon/DNA-RNA-Protein Translator mechanism

The inspectable method record for Codon/DNA-RNA-Protein Translator, kept separate from implementation and qualification.

Status: **VERIFIED_CLEAN**Lifecycle: **verified-clean**

## Model scope

Core algorithm is standard and correct when the standard genetic code, strand identity, orientation, frame indexing, incomplete-codon policy, and stop behavior are explicitly defined. Verdict is NEEDS_REVIEW because those interface semantics are missing from the specification, not because the standard codon lookup itself is incorrect.

- Triplet codon lookup using the NCBI standard genetic code (translation table 1) is correct for standard nuclear genetic code translation.

- The specification does not state whether DNA input is the coding strand or the template strand, nor whether the input is written 5-prime-to-3-prime or 3-prime-to-5-prime.

- The specification does not define whether reading_frame is zero-based or one-based, or whether frames are counted from the displayed input direction.

- The behavior for a sequence whose usable length is not a multiple of three is unspecified; the vectors below assume a trailing incomplete codon is ignored and reported.

- The behavior after the first stop codon is unspecified; the vectors below assume translation terminates at the first in-frame stop while mRNA output retains the full transcribed sequence.

- Handling of invalid symbols, lowercase input, ambiguous IUPAC bases, and internal whitespace is unspecified.

## Units and conventions

- There are no physical units; inputs are nucleotide strings.

- DNA coding-strand inputs are assumed to be written 5-prime-to-3-prime and are converted to mRNA by T-to-U substitution without reverse complementation.

- DNA template-strand inputs must be explicitly labeled and are assumed here to be written 3-prime-to-5-prime; mRNA is formed by complementary transcription and is written 5-prime-to-3-prime.

- RNA inputs are assumed already to be written 5-prime-to-3-prime and are not reverse-complemented.

- Reading frames in these vectors are zero-based offsets from the displayed 5-prime end for coding DNA and RNA; frame 0 starts at the first nucleotide and frame 1 at the second.

- Amino-acid output uses three-letter symbols and excludes the terminating stop codon; stop_codons identifies in-frame stop codons.

## Inspectable vector

One of 4 source-bound review vectors:

````
{
  "inputs": {
    "sequence": "ATGGCTTGGTAA",
    "sequence_type": "DNA_coding_strand",
    "orientation": "5_to_3",
    "reading_frame": 0
  },
  "expected_outputs": {
    "mrna_sequence": "AUGGCUUGGUAA",
    "codons_used": [
      "AUG",
      "GCU",
      "UGG",
      "UAA"
    ],
    "amino_acid_sequence": [
      "Met",
      "Ala",
      "Trp"
    ],
    "stop_codon_flags": [
      false,
      false,
      false,
      true
    ],
    "translation_terminated_at": "UAA"
  },
  "reference_data": {
    "standard_genetic_code": {
      "AUG": "Met",
      "GCU": "Ala",
      "UGG": "Trp",
      "UAA": "STOP",
      "source_convention": "NCBI Genetic Code, Translational Table 1, Standard Code"
    },
    "coding_DNA_to_mRNA": {
      "T": "U",
      "source_convention": "widely tabulated standard molecular-biology transcription convention"
    }
  },
  "working": "1. Coding DNA ATG GCT TGG TAA is written 5-prime-to-3-prime. 2. Replace each DNA T with RNA U: ATG GCT TGG TAA -> AUG GCU UGG UAA. 3. Look up codons: AUG -> Met; GCU -> Ala; UGG -> Trp; UAA -> STOP. 4. Emit amino acids before the stop: Met-Ala-Trp. 5. Stop flags by codon are false, false, false, true; translation terminates at UAA."
}
````

## Failure boundary

**BREAK_CLAIMED** · SELF_FLAGGED

The specification provides no stated resource limit or rejection behavior for extreme-length inputs, so a naive lookup implementation can fail through allocation or indexing exhaustion. It also leaves DNA strand orientation ambiguous, allowing the same written sequence to translate as different amino-acid sequences.

## Other records

[01**Overview**](<https://guthlabs.ai/docs/instruments/codon-dna-rna-protein-translator/>)[03**Implementation**](<https://guthlabs.ai/docs/instruments/codon-dna-rna-protein-translator/implementation/>)[04**Qualification**](<https://guthlabs.ai/docs/instruments/codon-dna-rna-protein-translator/qualification/>)

## Sources and evidence

These pointers bind the page to evidence. They do not grant authority or collapse verification into deployment.

- `VERIFIED_LEDGER.json`

- `evidence-tranche7/tranche7-results.json`

- `BOUNDARY_HAZARD_CATALOG.json`