Abstract
Tetrapods, unlike other organisms, have multimodal spectra of k-mers in their genomes
Highlights
The empirical frequencies of DNA k-mers in whole genome sequences provide an interesting perspective on genomic complexity, and the availability of large segments of genomic sequence from many organisms means that analysis of k-mers with non-trivial lengths is possible
The distribution of DNA k-mers (DNA 'words' of length k) namely, the k-mer spectrum - in whole genome sequences provides an interesting perspective on the complexity of the corresponding species
The CpG-containing k-mers wholly occupy the left-most areas, but are almost absent from the regions representing more abundant k-mers. There is no such clear effect for the species with unimodal distributions. These findings suggest the hypothesis that CpG suppression is what determines modality
Summary
The empirical frequencies of DNA k-mers in whole genome sequences provide an interesting perspective on genomic complexity, and the availability of large segments of genomic sequence from many organisms means that analysis of k-mers with non-trivial lengths is possible. The distribution of DNA k-mers (DNA 'words' of length k) namely, the k-mer spectrum - in whole genome sequences provides an interesting perspective on the complexity of the corresponding species. A number of theoretical investigations of genomic k-mer distributions were done prior to the sequencing of large genomes and these works suggested various plausible probabilistic models and parameters for such kmer distributions. Despite the relative abundance of sequenced genomes to date, the number of works investigating empirical k-mer distributions for values of k exceeding 2 or 3 is not very large. Reinert et al [2] discussed various plausible k-mer distributions, showing that the distribution for the number of occurrences of a particular k-mer in sequences generated from a hidden Markov model has two distinct large-sample regimes: a normal distribution for abundant k-mers, and a Poisson or compound Poisson distribution for extremely rare k-mers
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