Linkage Interval Map
Build additive genetic-map positions from ordered adjacent interval distances.
Description
An additive linkage map places ordered genes by consecutive genetic distances.
An additive linkage map places ordered genes by consecutive genetic distances. Centimorgan distances describe a genetic map rather than physical base-pair separation.
Build additive genetic-map positions from ordered adjacent interval distances.
When to use Linkage Interval Map
Use this for the following task: Build additive genetic-map positions from ordered adjacent interval distances.
Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
How to use Linkage Interval Map and understand its results
- Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
- Enter geneOrder, intervalDistancesCm, startPositionCm using the field table, then run the tool.
- Read mapPositionsCm, totalMapLengthCm. 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 |
|---|---|---|---|
| geneOrder | Gene order | list of string; each entry: string | Required |
| intervalDistancesCm | Interval distances cm | list of number; each entry: number | Required |
| startPositionCm | Start position cm | number | Required |
Supply at least two distinct ordered genes, one nonnegative distance per adjacent interval and a starting map position. Return cumulative positions and total interval length.1
position[i+1] = position[i]+intervalDistance[i] This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| mapPositionsCm | Map positions cm | list of number |
| totalMapLengthCm | Total map length cm | number |
{
"input": {
"geneOrder": [
"A",
"B",
"C"
],
"intervalDistancesCm": [
10,
20
],
"startPositionCm": 0
},
"output": {
"mapPositionsCm": [
0,
10,
30
],
"totalMapLengthCm": 30
}
}Limitations and assumptions
Distances are supplied rather than estimated or corrected for multiple crossovers.
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 Three Point Middle Gene for this operation: Resolve the middle gene from one-locus differences between parental and double-crossover haplotypes. For a complementary task, use Double Crossover Coincidence for this operation: Compare observed double crossovers with independent-interval expectation and compute interference.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Linkage Interval Map — tool.io
Similar or alternative tools
- Three Point Middle Gene
Resolve the middle gene from one-locus differences between parental and double-crossover haplotypes.
- Double Crossover Coincidence
Compare observed double crossovers with independent-interval expectation and compute interference.