Comparative genomic analysis of DNA motif frequency across the animal kingdom

The rapid expansion of genomic sequencing has produced vast datasets, yet the functional significance of non-coding DNA remains largely unexplored. Eukaryotic genomes contain numerous short, recurring DNA sequences known as motifs, which are crucial for gene regulation. In this study, it was hypothesized that the quantity of these regulatory motifs scales with the overall size of an organism’s genome. To test this, a high-performance computing approach was employed using a word count frequency algorithm to quantify 32 universal regulatory motifs across 51 diverse animal genomes. The analysis revealed a strong, positive linear correlation between the total motif count and genome size (R 2 = 0.9852). Regression analysis identified several motifs as significant predictors of genome size. Further investigation into key developmental motifs such as SOX2, SRY, POU5F1, and POU1F1 showed distinct distribution patterns across species. Together, these findings support the hypothesis that regulatory complexity, as approximated by motif frequency, increases with genome size and highlights the utility of computational methods in comparative genomics to uncover large-scale organizational properties of genomes.