Index measuring how 'random' the alignment strand has become.
Source:R/strand_randomisation_index.R
strand_randomisation_index.RdIn 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.
Arguments
- gb
A
GBreaksobject.- tiles
A number of tiles
Details
For each feature in the target genome, the total length of alignments on the plus strand is subtracted from that on the minus strand, and the absolute value is taken (because there is no guarantee that homologous chromosomes are sequenced in the same direction in different assemblies). This value is normalized by the total number of aligned bases. A weighted mean is then computed across all features, using each feature’s total aligned bases as its weight. 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. In 2025, a new tiles option
was added to make the index more robust to assembly errors and karyotype
changes.
References
Plessy C, Mansfield MJ, Bliznina A, Masunaga A, West C, Tan Y, Liu AW, Grašič J, Del Río Pisula MS, Sánchez-Serna G, Fabrega-Torrus M, Ferrández-Roldán A, Roncalli V, Navratilova P, Thompson EM, Onuma T, Nishida H, Cañestro C, Luscombe NM (2024). Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species. Genome Research, 34(3), 426–440. https://doi.org/10.1101/gr.278295.123. PMID: 38621828
See also
Other Similarity indexes:
F81_distance(),
GOC(),
HKY85_distance(),
JC69_distance(),
K80_distance(),
P_distance(),
T92_distance(),
TN93_distance(),
correlation_index(),
karyotype_index(),
logDet_distance(),
slidingWindow(),
synteny_index(),
tau_index()