Synteny Order Conservation
Score directional adjacent-gene order conservation between supplied syntenic blocks.
Description
Synteny concerns conserved genomic neighborhoods.
Synteny concerns conserved genomic neighborhoods. A directional adjacency score measures whether neighboring reference genes remain adjacent in the same order.
Score directional adjacent-gene order conservation between supplied syntenic blocks.
When to use Synteny Order Conservation
Use this for the following task: Score directional adjacent-gene order conservation between supplied syntenic blocks.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Synteny Order Conservation 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 referenceOrder, comparisonOrder using the field table, then run the tool.
- Read conservedAdjacentPairs, possibleAdjacentPairs, collinearityFraction. 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 |
|---|---|---|---|
| referenceOrder | Reference order | list of string; minimum entries 2; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S | Required |
| comparisonOrder | Comparison order | list of string; minimum entries 0; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S | Required |
Require distinct gene IDs in each list. Map comparison positions and count a reference pair only when its second gene immediately follows its first in the comparison.1
fraction = conserved directional adjacent pairs/(referenceGeneCount−1) This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| conservedAdjacentPairs | Adjacent reference pairs retained in the same direction in comparisonOrder. | integer |
| possibleAdjacentPairs | Possible adjacent pairs | integer |
| collinearityFraction | Collinearity fraction | number |
{
"input": {
"referenceOrder": [
"A",
"B",
"C",
"D"
],
"comparisonOrder": [
"A",
"B",
"D",
"C"
]
},
"output": {
"conservedAdjacentPairs": 1,
"possibleAdjacentPairs": 3,
"collinearityFraction": 0.3333333333333333
}
}Limitations and assumptions
Reversed adjacency is not conserved here. The supplied blocks and homolog assignments are not inferred.
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 Reciprocal Best Hit Pairs for this operation: Validate reciprocal best-hit gene pairs from independently supplied forward and reverse maps. For a complementary task, use Paralog Age Peaks for this operation: Detect strict interior peaks in a supplied paralog-age histogram as candidate duplication signals.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Synteny Order Conservation — tool.io
Similar or alternative tools
- Reciprocal Best Hit Pairs
Validate reciprocal best-hit gene pairs from independently supplied forward and reverse maps.
- Paralog Age Peaks
Detect strict interior peaks in a supplied paralog-age histogram as candidate duplication signals.