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Identification of different sequence properties between HIV-1 DNA and RNA across subtypes using the k-mer-based approach

Chen, H.-C.; Wisniewski, J.; Serwin, K.; Parczewski, M.; Kula-Pacurar, A.; Skums, P.; Kirpich, A.; Yakovlev, S.

2026-02-26 bioinformatics
10.64898/2026.02.25.707904 bioRxiv
Show abstract

Advanced analytical tools that enable mining of the masked features hidden in intricate datasets and strengthening the biological interpretation of multigenomic outputs hold paramount importance. In this study, we present an updated version of a k-mer-based approach, PORT-EK-v2, allowing for a comparison of multiple genomic datasets and identification of over-represented genomic regions, k-mers, related to specific organisms. Using PORT-EK-v2, we exemplified that most likely DNA and RNA sequence properties are distinct across HIV-1 subtypes. Furthermore, we showcased that "isolate k-mer count" could serve as a default choice in classifying the DNA versus RNA sequence property. Lastly, results based on Markov chain Monte Carlo modeling unveiled a discontinuous nature of the sequence property in terms of k-mer frequencies across HIV-1 subtypes. Altogether, we propose that the sequence property (DNA versus RNA) is distinct across HIV-1 subtypes and has a consequential impact on identifying new and emerging subtypes in the future.

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