Abstract
A new algorithm has been constructed for finding under- and overrepresented oligonucleotide motifs in the protein coding regions of genomes that have been normalized for G/C content, codon usage, and amino acid order. This Robins-Krasnitz algorithm has been employed to compare the oligonucleotide frequencies between many different prokaryotic genomes. Evidence is presented demonstrating that at least some of these sequence motifs are functionally important and selected for or against during the evolution of these prokaryotes. The applications of this method include the optimization of protein expression for synthetic genes in foreign organisms, identification of novel oligonucleotide signals used by the organism and the examination of evolutionary relationships not dependent upon different gene sequence trees.
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