Six Frame ORF Scan

Find the longest complete ATG-to-stop ORF across six frames using the standard genetic code, with original-strand half-open coordinates including the stop.

Description

An open reading frame can be sought on either DNA strand and in three offsets on each.

An open reading frame can be sought on either DNA strand and in three offsets on each. A complete ATG-to-stop run is a specific sequence pattern, not proof of expression.^[1]

Find the longest complete ATG-to-stop ORF across six frames using the standard genetic code, with original-strand half-open coordinates including the stop.

When to use Six Frame ORF Scan

Use this for the following task: Find the longest complete ATG-to-stop ORF across six frames using the standard genetic code, with original-strand half-open coordinates including the stop.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use Six Frame ORF Scan and understand its results

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
Enter sequence using the field table, then run the tool.
Read strand, frame, startIndex, endIndex, codingBases, aminoAcidCount. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
sequence	Sequence	string; minimum text length 1; maximum text length 1000000; pattern ^\s[ACGTacgt]+\s$	Required

Scan forward and reverse-complement strands with the standard ATG start and TAA/TAG/TGA stops. Keep the longest complete ORF, retaining the first traversal tie. Return original-strand half-open coordinates including the stop; frame is 0–2 on the chosen strand.^[2]

codingBases = stopStart − ATGstart; aminoAcidCount = codingBases/3

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
strand	Strand	string
frame	Frame offset 0, 1, or 2 on the selected strand; -1 if absent. Equal lengths choose forward before reverse, then lower frame, then earlier start on that strand.	integer
startIndex	Zero-based inclusive coordinate in the trimmed original sequence; -1 if absent.	integer
endIndex	Zero-based exclusive coordinate including the stop codon in the original sequence; -1 if absent.	integer
codingBases	Bases from ATG through the last sense codon; excludes the terminal stop codon.	integer
aminoAcidCount	Amino acid count	integer

json

{
  "input": {
    "sequence": "TTATTTCAT"
  },
  "output": {
    "strand": "reverse",
    "frame": 0,
    "startIndex": 0,
    "endIndex": 9,
    "codingBases": 6,
    "aminoAcidCount": 2
  }
}

Limitations and assumptions

codingBases excludes the stop although endIndex includes it. When no complete ORF is found, strand is none and indices/frame are −1. Alternative codes, starts and incomplete ORFs are excluded.

The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose Coding Frame Integrity for this operation: Screen an in-frame canonical DNA coding sequence using the standard ATG start and TAA/TAG/TGA stops, with chosen start/terminal-stop requirements. For a complementary task, use Premature Stop Position for this operation: Check a codon replacement for a new premature stop under the standard genetic code.

Further background: Background specification: Six Frame ORF Scan.

References

Background specification: Six Frame ORF Scan — NCBI
Six Frame ORF Scan — tool.io

Similar or alternative tools

Coding Frame Integrity
Screen an in-frame canonical DNA coding sequence using the standard ATG start and TAA/TAG/TGA stops, with chosen start/terminal-stop requirements.
Premature Stop Position
Check a codon replacement for a new premature stop under the standard genetic code.