Phylogenetic Footprinting Based on Harmonic Clustering and Classification Algorithm

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regions from multiple species, and reliable proteins classification is necessary for the identification of orthologous regions. There are two major grouping methods, i.e. classification and clustering, and classification needs prior-knowledge, while clustering bases on the sequence similarity. In practice, the results of classification and clustering are often inconsistent. For this problem, this paper proposed harmonic clustering-classification algorithm, by this algorithm, the results of classification and clustering keep high consistency, then according to the classification, phylogenetic footprinting was implemented on Azospirillum species and its orthologous strains, and compared to the traditional methods, the results were more useful and reliable.