Identification of Orthologous Lsr Systems through An Iterative Synteny-Based Search

Most strategies employed for ferreting out conserved orthologous genomic modules in prokaryotes use synteny, conservation in gene order frequently between two to four genes resulting in what has been referred to as a gene string. The solution proffered here differs from the standard solutions in that the search begins with a single template, considers homologous hits beyond the highest, and uses an iterative scheme where genomes containing gene strings that scored well on synteny but not on orthologous homology against the template are themselves used as templates in later steps. Single iterations are compared against the similarity of the genome background via monte carlo simulations of randomly selected gene strings of coincident length. The method is applied to the LacI system and new putative organisms containing the less well defined quorum sensing system, Lsr are proposed. This set is more expansive than that proposed by standard software such as STRING.