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.
Description
A coding-frame screen checks codon alignment and stop placement.
A coding-frame screen checks codon alignment and stop placement. The standard ATG start and three standard stop codons define this tool’s sequence profile.1
Screen an in-frame canonical DNA coding sequence using the standard ATG start and TAA/TAG/TGA stops, with chosen start/terminal-stop requirements.
When to use Coding Frame Integrity
Use this for the following task: Screen an in-frame canonical DNA coding sequence using the standard ATG start and TAA/TAG/TGA stops, with chosen start/terminal-stop requirements.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Coding Frame Integrity 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, requireStartCodon, requireTerminalStop using the field table, then run the tool.
- Read frameDivisible, internalStopCount, intact. 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 |
| requireStartCodon | Require start codon | boolean | Required |
| requireTerminalStop | Require terminal stop | boolean | Required |
Normalize canonical DNA, inspect codons from offset zero, and count complete stops before the last codon. Require enough sequence to contain a sense codon; optionally require ATG and a terminal stop.2
intact = divisible by 3 AND no internal stops AND requested boundary codons satisfied This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| frameDivisible | Frame divisible | boolean |
| internalStopCount | Internal stop count | integer |
| intact | Intact | boolean |
{
"input": {
"sequence": "ATGAAATAA",
"requireStartCodon": true,
"requireTerminalStop": true
},
"output": {
"frameDivisible": true,
"internalStopCount": 0,
"intact": true
}
}Limitations and assumptions
No alternative genetic code, splice model or expression evidence is evaluated. Flags can be false for correctly supplied DNA.
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 Six Frame ORF Scan for this operation: 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. 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: Coding Frame Integrity.
References
-
Coding Frame Integrity — tool.io
Similar or alternative tools
- 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.
- Premature Stop Position
Check a codon replacement for a new premature stop under the standard genetic code.