Alignment Identity Gate
Gate segmental-duplication alignment identity including single-gap columns as mismatches.
Description
Alignment identity depends on which columns count in the denominator.
Alignment identity depends on which columns count in the denominator. Here a gap against a base is a mismatch, while a double-gap column is invalid.
Gate segmental-duplication alignment identity including single-gap columns as mismatches.
When to use Alignment Identity Gate
Use this for the following task: Gate segmental-duplication alignment identity including single-gap columns as mismatches.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Alignment Identity Gate 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 firstAlignment, secondAlignment, minimumIdentityFraction using the field table, then run the tool.
- Read comparedColumns, matchingColumns, identityFraction, passes. 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 |
|---|---|---|---|
| firstAlignment | First alignment | string; minimum text length 1; maximum text length 1000000; pattern ^[ACGTacgt-]+(?![\s\S]) | Required |
| secondAlignment | Second alignment | string; minimum text length 1; maximum text length 1000000; pattern ^[ACGTacgt-]+(?![\s\S]) | Required |
| minimumIdentityFraction | Matching nongap bases divided by all columns; single-gap columns count as mismatches. | number; minimum 0; maximum 1 | Required |
Supply equal-length supported aligned strings and a fraction threshold. Normalize case, reject double gaps and test identity inclusively against the minimum.1
identity = matching nongap columns/all alignment columns This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| comparedColumns | Compared columns | integer |
| matchingColumns | Matching columns | integer |
| identityFraction | Identity fraction | number |
| passes | Passes | boolean |
{
"input": {
"firstAlignment": "AC-GT",
"secondAlignment": "ACTGT",
"minimumIdentityFraction": 0.9
},
"output": {
"comparedColumns": 5,
"matchingColumns": 4,
"identityFraction": 0.8,
"passes": false
}
}Limitations and assumptions
No alignment is constructed or evolutionary model fitted. The declared gap convention can differ from other tools.
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 CIGAR Operation Summary for this operation: Summarize CIGAR operations and distinguish query-consuming and reference-consuming bases. For a complementary task, use Kaks Selection Screen for this operation: Screen a Ka/Ks ratio relative to a caller-defined neutral band without claiming statistical significance.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Alignment Identity Gate — tool.io
Similar or alternative tools
- CIGAR Operation Summary
Summarize CIGAR operations and distinguish query-consuming and reference-consuming bases.
- Kaks Selection Screen
Screen a Ka/Ks ratio relative to a caller-defined neutral band without claiming statistical significance.