Base-Base Correlation a Novel Sequence Feature and its Applications

Base-base correlation (BBC), as a novel sequence feature, reflects genome information structure. BBC has been applied to distinguish various functional regions of genomes. Meanwhile, as a genomic signature, BBC is used to compare sequences from different species. The database based on BBC feature has been constructed to search for similar sequences. It has been found that BBC carries a strong phylogenetic signal. We applied BBC to virus genotyping and whole genome prokaryotic phylogeny. Compared with traditional alignment-based phylogenetic analysis, the algorithm based on BBC is a normalization operation to compare genomes of different scales, which are difficult to obtain a good sequence alignment. In addition, the algorithm based on BBC has lower time complexity than the one based on alignment.