Reciprocal Best Hit Pairs
Validate reciprocal best-hit gene pairs from independently supplied forward and reverse maps.
Description
Reciprocal best hits are gene pairs selected in both directional searches.
Reciprocal best hits are gene pairs selected in both directional searches. Independent forward and reverse hit maps are needed to check reciprocity.
Validate reciprocal best-hit gene pairs from independently supplied forward and reverse maps.
When to use Reciprocal Best Hit Pairs
Use this for the following task: Validate reciprocal best-hit gene pairs from independently supplied forward and reverse maps.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Reciprocal Best Hit Pairs 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 queryGenes, forwardHits, targetGenes, reverseHits using the field table, then run the tool.
- Read reciprocalQueries, reciprocalTargets, pairCount. 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 |
|---|---|---|---|
| queryGenes | Query genes | list of string; minimum entries 0; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S | Required |
| forwardHits | Forward hits | list of string; minimum entries 0; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S | Required |
| targetGenes | Target genes | list of string; minimum entries 0; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S | Required |
| reverseHits | Reverse hits | list of string; minimum entries 0; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S | Required |
Align distinct query/target identifiers with their respective best-hit lists. Look up reverse hits for each forward target and emit reciprocal pairs in query order.1
pair accepted when reverseHit[forwardHit[query]] == query This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| reciprocalQueries | Reciprocal queries | list of string |
| reciprocalTargets | Reciprocal targets | list of string |
| pairCount | Pair count | integer |
{
"input": {
"queryGenes": [
"A",
"B"
],
"forwardHits": [
"X",
"Y"
],
"targetGenes": [
"X",
"Y"
],
"reverseHits": [
"A",
"C"
]
},
"output": {
"reciprocalQueries": [
"A"
],
"reciprocalTargets": [
"X"
],
"pairCount": 1
}
}Limitations and assumptions
Sequence searches, score ties and orthology validation are not performed. Reciprocity alone is not proof of orthology.
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 Synteny Order Conservation for this operation: Score directional adjacent-gene order conservation between supplied syntenic blocks. 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
-
Reciprocal Best Hit Pairs — tool.io
Similar or alternative tools
- Synteny Order Conservation
Score directional adjacent-gene order conservation between supplied syntenic blocks.
- Paralog Age Peaks
Detect strict interior peaks in a supplied paralog-age histogram as candidate duplication signals.