A Genome Signature Based on Markov Modeling

We propose a "genome signature" for bacterial genomes based on a triplets Markov model. Without the alignment or data preprocessing required by traditional analysis methods, the model is shown to efficiently capture identifying genomic information at genus, species and strain levels. Based on the model, a simple distance measure is proposed for constructing phylogeny trees. Unlike other genome signatures based on word frequency with problems balancing word length and window size, the method has been shown to work successfully with both bacterial whole genome data and individual eukaryotic genes. Applications of the model to phylogenetic analysis and sequence fragment identification are presented