Kaks Selection Screen
Screen a Ka/Ks ratio relative to a caller-defined neutral band without claiming statistical significance.
Description
The nonsynonymous-to-synonymous rate ratio provides a coarse selection screen.
The nonsynonymous-to-synonymous rate ratio provides a coarse selection screen. A tolerance around one separates descriptive bands without establishing significance.
Screen a Ka/Ks ratio relative to a caller-defined neutral band without claiming statistical significance.
When to use Kaks Selection Screen
Use this for the following task: Screen a Ka/Ks ratio relative to a caller-defined neutral band without claiming statistical significance.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Kaks Selection Screen 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 nonsynonymousRate, synonymousRate, neutralTolerance using the field table, then run the tool.
- Read kaksRatio, selectionBand. 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 |
|---|---|---|---|
| nonsynonymousRate | Nonsynonymous rate | number; minimum 0 | Required |
| synonymousRate | Synonymous rate | number; greater than 0 | Required |
| neutralTolerance | Neutral tolerance | number; minimum 0; maximum 1 | Required |
Use a nonnegative nonsynonymous rate, positive synonymous rate and tolerance in [0,1]. Classify below 1−tolerance, above 1+tolerance, or inside the inclusive neutral band.1
Ka/Ks = nonsynonymousRate/synonymousRate This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| kaksRatio | Kaks ratio | number |
| selectionBand | Selection band | string |
{
"input": {
"nonsynonymousRate": 0.02,
"synonymousRate": 0.1,
"neutralTolerance": 0.1
},
"output": {
"kaksRatio": 0.19999999999999998,
"selectionBand": "below-neutral"
}
}Limitations and assumptions
Rates must be estimated independently. No likelihood test, correction for saturation or confidence interval is performed.
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 Synonymous Clock Divergence for this operation: Estimate divergence time from dS assuming equal constant substitution rates on both lineages. For a complementary task, use Synonymous Codon Sites for this operation: Count equally weighted synonymous single-base alternatives by codon position using the standard code.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Kaks Selection Screen — tool.io
Similar or alternative tools
- Synonymous Clock Divergence
Estimate divergence time from dS assuming equal constant substitution rates on both lineages.
- Synonymous Codon Sites
Count equally weighted synonymous single-base alternatives by codon position using the standard code.