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bioRxiv · 10.1101/2021.10.12.464028

HORmon: automated annotation of human centromeres

Kunyavskaya, O.·Dvorkina, T.·Bzikadze, A. V.·Alexandrov, I.·Pevzner, P. A.
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Abstract

Recent advances in long-read sequencing opened a possibility to address the long-standing questions about the architecture and evolution of human centromeres. They also emphasized the need for centromere annotation (partitioning human centromeres into monomers and higher-order repeats (HORs)). Even though there was a half-century-long series of semi-manual studies of centromere architecture, a rigorous centromere annotation algorithm is still lacking. Moreover, an automated centromere annotation is a prerequisite for studies of genetic diseases associated with centromeres, and evolutionary studies of centromeres across multiple species. Although the monomer decomposition (transforming a centromere into a monocentromere written in the monomer alphabet) and the HOR decomposition (representing a monocentromere in the alphabet of HORs) are currently viewed as two separate problems, we demonstrate that they should be integrated into a single framework in such a way that HOR (monomer) inference affects monomer (HOR) inference. We thus developed the HORmon algorithm that integrates the monomer/HOR inference and automatically generates the human monomers/HORs that are largely consistent with the previous semi-manual inference.

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Kunyavskaya, O., Dvorkina, T., Bzikadze, A. V., Alexandrov, I., Pevzner, P. A.. 2021-10-12. HORmon: automated annotation of human centromeres. https://doi.org/10.1101/2021.10.12.464028

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