SELF-IDENTIFICATION OF PROTEIN-CODING REGIONS IN MICROBIAL GENOMES

A new method for predicting protein-coding regions in microbial genomi c DNA sequences is presented. It uses an ab initio iterative Markov mo deling procedure to automatically perform the partition of genomic seq uences into three subsets shown to correspond to coding, coding on the opposite strand, and noncoding segments. In contrast to current metho ds, such as GENEMARK [Borodovsky, M. & McIninch, J. D. (1993) Comput. Chern. 17, 123-133], no training set or prior knowledge of the statist ical properties of the studied genome are required. This new method to lerates error rates of 1-2% and can process unassembled sequences. It is thus ideal for the analysis of genome survey and/or fragmented sequ ence data from uncharacterized microorganisms. The method was validate d on 10 complete bacterial genomes (from four major phylogenetic linea ges). The results show that protein-coding regions can be identified w ith an accuracy of up to 90% with a totally automated and objective pr ocedure.