Description

Non-B DNA motifs annotation

Methods

Non-B motifs of A-phased repeats (APR), direct repeats (DR), inverted repeats (IR), mirror repeats (MR), short tandem repeats (STR) and Z-DNA (Z) were annotated using gfa (https://github.com/abcsFrederick/non-B_gfa), described in detail in: https://github.com/kxk302/non-B_gfa.
Triplex motifs (TRI) is a subset of mirror repeats with spacer length <= 8 bp and a minimum Pyrimidine/Purine content of 10%, flagged by gfa as "subset=1".
G-quadruplex motifs (GQ) were annotated with Quadron (https://github.com/aleksahak/Quadron/tree/master), using a docker image found in: https://github.com/kxk302/Quadron_Docker. Quadron scores are not integers as required by bed format, so the score is rounded to the closest integer. The exact value is given in the 4th bed column.

Credits

Kateryna Makova<kdm16@psu.edu>, Linnéa Smeds, Kaivan Kamali

References

Smeds, L., Kamali, K., Kejnovska, I., Kejnovsky, E., Chiaromonte, F., Makova, K.D. Non-canonical DNA in human and other ape telomere-to-telomere genomes. bioRxiv (2024). https://doi.org/10.1101/2024.09.02.610891v2

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G.A., [..] Makova, K.D., Phillippy, A.M., Eichler, E.E. Complete sequencing of ape genomes. bioRxiv (2024). https://doi.org/10.1101/2024.07.31.605654

https://github.com/makovalab-psu/T2T_primate_nonB