Three Point Middle Gene

Resolve the middle gene from one-locus differences between parental and double-crossover haplotypes.

Description

In a three-point cross, a double-crossover haplotype differs from its corresponding parental haplotype at the middle locus.

In a three-point cross, a double-crossover haplotype differs from its corresponding parental haplotype at the middle locus. Consistent differences can identify the middle gene.

Resolve the middle gene from one-locus differences between parental and double-crossover haplotypes.

When to use Three Point Middle Gene

Use this for the following task: Resolve the middle gene from one-locus differences between parental and double-crossover haplotypes.

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.

How to use Three Point Middle Gene and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter geneNames, parentalHaplotypes, doubleCrossoverHaplotypes using the field table, then run the tool.
Read middleGene, middleIndex. 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
geneNames	Gene names	list of string; each entry: string	Required
parentalHaplotypes	Parental haplotypes	list of string; each entry: string	Required
doubleCrossoverHaplotypes	Double crossover haplotypes	list of string; each entry: string	Required

Use three gene names, two three-character parent haplotypes and at least one double-crossover haplotype. Require each DCO to differ at one locus from exactly one parent and all inferred loci to agree.^[1]

middleIndex = unique one-locus difference shared by all supplied DCO haplotypes

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
middleGene	Middle gene	string
middleIndex	Middle index	number

json

{
  "input": {
    "geneNames": [
      "A",
      "B",
      "C"
    ],
    "parentalHaplotypes": [
      "ABC",
      "abc"
    ],
    "doubleCrossoverHaplotypes": [
      "AbC",
      "aBc"
    ]
  },
  "output": {
    "middleGene": "B",
    "middleIndex": 1
  }
}

Limitations and assumptions

The tool does not decide which observed classes are parental or DCO classes. Ambiguous and disagreeing patterns are rejected.

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 Linkage Interval Map for this operation: Build additive genetic-map positions from ordered adjacent interval distances. 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

Three Point Middle Gene — tool.io

Similar or alternative tools

Linkage Interval Map
Build additive genetic-map positions from ordered adjacent interval distances.
Double Crossover Coincidence
Compare observed double crossovers with independent-interval expectation and compute interference.