UCSF

Periodicity in nucleotide sequences arises from regular repeating patterns that may reflect important structure and function. Although a three-base periodicity in coding regions has been known for some time and has been used as the basis for powerful gene prediction algorithms, its origins are still not fully understood. Here we show that, contrary to common belief, amino acid bias and codon usage bias are insucient to create base-three periodicity. This paper rigorously applies the method of spectral envelope to systematically characterize the contributions of codon bias, amino acid bias, and protein structural motifs to the three-base periodicity of coding sequences. Additionally, we show how the method of spectral envelope can be used to trace the evolution of viral genomes and monitor global sequence changes without having to align to previously known genomes. This method also detects reassortment events, such as those that led to the 2009 pandemic H1N1 virus.