Indel Frame Phase
Classify net indel coding-phase disruption by modulo three.
Description
A coding insertion/deletion changes reading-frame phase according to its net length modulo three.
A coding insertion/deletion changes reading-frame phase according to its net length modulo three. The sign of length change describes insertion versus deletion.
Classify net indel coding-phase disruption by modulo three.
When to use Indel Frame Phase
Use this for the following task: Classify net indel coding-phase disruption by modulo three.
Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
How to use Indel Frame Phase and understand its results
- Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
- Enter insertedBases, deletedBases using the field table, then run the tool.
- Read netLengthChange, phaseShift, frameshift. 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 |
|---|---|---|---|
| insertedBases | Inserted bases | integer | Required |
| deletedBases | Deleted bases | integer | Required |
Supply nonnegative integer inserted/deleted lengths. Normalize the remainder to 0–2 and flag nonzero phase as frameshift.1
net = inserted−deleted; phase = ((net mod 3)+3) mod 3 This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| netLengthChange | Net length change | number |
| phaseShift | Phase shift | number |
| frameshift | Frameshift | boolean |
{
"input": {
"insertedBases": 4,
"deletedBases": 1
},
"output": {
"netLengthChange": 3,
"phaseShift": 0,
"frameshift": false
}
}Limitations and assumptions
A net multiple of three is not proof of functional neutrality. Location, codon changes and splice effects are excluded.
The tool evaluates supplied observations or a declared model. It does not establish the biological cause of an observed pattern. 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 Premature Stop Position for this operation: Check a codon replacement for a new premature stop under the standard genetic code. For a complementary task, use 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.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Indel Frame Phase — tool.io
Similar or alternative tools
- Premature Stop Position
Check a codon replacement for a new premature stop under the standard genetic code.
- 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.