Doublet frequencies in sequenced nucleic acids

Abstract

A doublet frequency count (set of frequencies of the 16 possible two-base sequences) can be calculated from the experimentally determined overall sequence of a nucleic acid. In this paper, a statistical methodology is developed for comparing such counts with random, with others of the same type or with doublet proportions found in whole DNAs. The methods are applied to two major categories of sequenced RNAs. It is found that vertebrate ribosomal and transfer RNAs show significant differences from the overall vertebrate DNA pattern, especially in the frequency of the doublet CG. Bacterial rRNA and tRNA, on the other hand, show less dissimilarity from total DNA. In the RNA of the small bacteriophage MS2, the doublet frequencies of the translated regions of the genome resemble those in the host E. coli, whereas those in the intercistronic regions differ substantially. All these findings are discussed in relation to the origin, evolution and selection of the nucleic acids concerned.