Index representing how 'syntenic' two genomes are

A sequence feature on the target genome will be considered ‘syntenic’ if most of its alignments map to the same feature of the query genome, and the two genomes are considered syntenic if most of their features are syntenic.

Usage

synteny_index(gb)

Arguments

gb

A GBreaks object.

Value

Returns a numeric value between 0 and 1.

Details

For a given feature of the target genome the number of bases aligned on each of the features of the query genome are computed. The largest number is taken. 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

Here, the definition of ‘synteny’ is sequences on the same DNA strands, or in technical terms: sequences that are on the same feature, regardless of strand orientation.

See also

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

Examples

gb       <- GRanges(c("Ref:100-200:+",   "Ref:400-500:+",    "Ref:600-700:+"))
gb$query <- GRanges(c("Que:1100-1200:+", "Que2:1700-1800:+", "Que:1500-1600:+"))
synteny_index(gb)
#> [1] 0.6666667