Genomic Signatures from DNA Word Graphs

Genomes have both deterministic and random aspects, with the underlying DNA sequences exhibiting features at numerous scales, from codons and cis-elements through genes and on to regions of conserved or divergent gene order. The DNAWords program aims to identify mathematical structures that characterize genomes at multiple scales. The focus of this work is the fine structure of genomic sequences, the manner in which short nucleotide sequences fit together to comprise the genome as an abstract sequence, within a graph-theoretic setting. A DNA word graph is a generalization of a de Bruijn graph that records the occurrence counts of node and edges in a genomic sequence. A DNA word graph can be derived from a genomic sequence generated by a finite Markov chain or a subsequence of a sequenced genome. Both theoretically and empirically, DNA word graphs give rise to genomic signatures. Several genomic signatures are derived from the structure of a DNA word graph, including an information-rich and visually appealing genomic bar code. Application of genomic signatures to several genomes demonstrate their practical value in identifying and distinguishing genomic sequences.