Restriction Enzyme Cut Site Finder implementation

Binding contract

This record describes what an executable surface must bind and validate. It does not claim that a public calculator, package, or production route is deployed.

Record owner

Guth Instruments

Lifecycle

verified-clean

Evidence ID

t7-095

Effect

Computation or source lookup only

Input and validation requirements

The specification does not define coordinate indexing, cleavage-boundary reporting, empty-input behavior, fragment-list behavior for zero cuts, or enzyme cleavage offsets. A caller could therefore receive incompatible but superficially plausible outputs. The extreme-length vector also exposes possible runtime or memory failure even though the expected arithmetic result is well-defined.

Required corrections

No binding erratum is attached to this unique-name record. Implementers must still preserve the declared units, domain, and failure behavior.

Inspectable interface fixture

The sample below is evidence for interface and validation tests, not a production implementation.

{
  "inputs": {
    "dna_sequence": "TTTGAATTCCGA",
    "enzyme": "EcoRI"
  },
  "expected_outputs": {
    "recognition_site_positions": [
      4
    ],
    "cut_positions": [
      4
    ],
    "fragment_lengths": [
      4,
      8
    ]
  },
  "reference_data": {
    "enzyme": "EcoRI",
    "recognition_site": "GAATTC",
    "cut_notation": "G^AATTC",
    "iupac_interpretation": "No ambiguity codes; exact matching",
    "source_convention": "REBASE/common textbook restriction-enzyme convention; widely tabulated standard value"
  },
  "working": "Sequence length = 12 nucleotides. The substring at positions 4-9 is GAATTC, so the recognition-site start is 4. EcoRI cuts G^AATTC, after nucleotide 4, giving cut coordinate 4. Fragment 1 length = 4 - 0 = 4. Fragment 2 length = 12 - 4 = 8. Therefore fragments = [4, 8]."
}

Other records

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