Source: https://guthlabs.ai/docs/instruments/restriction-enzyme-cut-site-finder/mechanism/

instrument mechanism / verified-clean

# Restriction Enzyme Cut Site Finder mechanism

The inspectable method record for Restriction Enzyme Cut Site Finder, kept separate from implementation and qualification.

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

## Model scope

The recognition-site matching concept is valid, and the honest-label statement appropriately identifies the table as a non-exhaustive reference subset. The instrument needs explicit position indexing, cleavage offsets, strand handling, topology, invalid-input behavior, and unsupported-enzyme behavior before its outputs are unambiguous.

- Pattern matching against recognition motifs is the standard algorithm, provided IUPAC symbols are interpreted correctly (for example, N means A, C, G, or T).

- The specification does not define enzyme-specific cleavage offsets, which are required to compute cut positions and fragment lengths; recognition-site matching alone is insufficient.

- The specification does not state whether matching includes the reverse-complement strand. This matters for non-palindromic recognition sites and enzymes with asymmetric cleavage behavior.

- The specification does not define whether sequences are linear or circular, nor the position convention (1-based versus 0-based and whether a reported position is the recognition-site start or the cleavage coordinate).

## Units and conventions

- DNA positions are assumed to be 1-based nucleotide coordinates.

- A reported recognition-site position is the 1-based start coordinate of the matched motif.

- A reported cut coordinate is the number of nucleotides to the left of the cleavage point in a linear sequence.

- Fragment lengths are measured in nucleotides.

- All test vectors assume a linear, double-stranded DNA sequence and the listed enzyme cut convention.

## Inspectable vector

One of 4 source-bound review vectors:

````
{
  "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]."
}
````

## Failure boundary

**BREAK_CLAIMED** · SELF_FLAGGED

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.

## Other records

[01**Overview**](<https://guthlabs.ai/docs/instruments/restriction-enzyme-cut-site-finder/>)[03**Implementation**](<https://guthlabs.ai/docs/instruments/restriction-enzyme-cut-site-finder/implementation/>)[04**Qualification**](<https://guthlabs.ai/docs/instruments/restriction-enzyme-cut-site-finder/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`