Revealing the Shape of Genome Space via K-mer Topology
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arXiv
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| Format: | Preprint |
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2024
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| _version_ | 1866910766261600256 |
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| author | Hozumi, Yuta Wei, Guo-Wei |
| author_facet | Hozumi, Yuta Wei, Guo-Wei |
| contents | Despite decades of effort, understanding the shape of genome space in biology remains a challenge due to the similarity, variability, diversity, and plasticity of evolutionary relationships among species, genes, or other biological entities. We present a k-mer topology method, the first of its kind, to delineate the shape of the genome space. K-mer topology examines the topological persistence and the evolution of the homotopic shape of the sequences of k nucleotides in species, organisms, and genes using persistent Laplacians, a new multiscale combinatorial approach. We also propose a topological genetic distance between species by their topological invariants and non-harmonic spectra over scales. This new metric defines the topological phylogenetic trees of genomes, facilitating species classification and clustering. K-mer topology substantially outperforms state-of-the-art methods on a variety of benchmark datasets, including mammalian mitochondrial genomes, Rhinovirus, SARS-CoV-2 variants, Ebola virus, Hepatitis E virus, Influenza hemagglutinin genes, and whole bacterial genomes. K-mer topology reveals the intrinsic shapes of the genome space and can be directly applied to the rational design of viral vaccines. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2412_20202 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Revealing the Shape of Genome Space via K-mer Topology Hozumi, Yuta Wei, Guo-Wei Genomics Algebraic Topology Despite decades of effort, understanding the shape of genome space in biology remains a challenge due to the similarity, variability, diversity, and plasticity of evolutionary relationships among species, genes, or other biological entities. We present a k-mer topology method, the first of its kind, to delineate the shape of the genome space. K-mer topology examines the topological persistence and the evolution of the homotopic shape of the sequences of k nucleotides in species, organisms, and genes using persistent Laplacians, a new multiscale combinatorial approach. We also propose a topological genetic distance between species by their topological invariants and non-harmonic spectra over scales. This new metric defines the topological phylogenetic trees of genomes, facilitating species classification and clustering. K-mer topology substantially outperforms state-of-the-art methods on a variety of benchmark datasets, including mammalian mitochondrial genomes, Rhinovirus, SARS-CoV-2 variants, Ebola virus, Hepatitis E virus, Influenza hemagglutinin genes, and whole bacterial genomes. K-mer topology reveals the intrinsic shapes of the genome space and can be directly applied to the rational design of viral vaccines. |
| title | Revealing the Shape of Genome Space via K-mer Topology |
| topic | Genomics Algebraic Topology |
| url | https://arxiv.org/abs/2412.20202 |