Index measuring how 'random' the alignment strand has become.

In groups of species where major changes of gene order happened but genes tended to stay on the same chromosome, a marked feature is that the strand on which homologous sequences align appears to be randomised. This index expresses it with a number.

Usage

strand_randomisation_index(gb)

Arguments

gb

A GBreaks object.

Value

Returns a numeric value between 0 and 1.

Details

For each feature of the target genome, the total length of its alignments on the plus strand is subtracted from the total length of its alignments on the minus strand. The sign of this number is removed because there is no guarantee that homologous chromosomes are sequenced in the same direction in different assemblies. To make features comparable, this number is then normalised by total number of aligned bases. Then, the computed numbers for all the target's features are averaged with a weighted mean, where the weight is the total number of aligned bases of that feature. Thus, a number close to 1 is expected for closely related genomes.

Note

This index is designed for comparison of chromosomal assemblies that have a strong conservation of synteny in the sense most homologous genes are mapped on pairs of homologous chromosomes.

See also

Other Similarity indexes: GOC(), correlation_index(), synteny_index()

Examples

strand_randomisation_index(exampleInversion)
#> [1] 0.3992674