335Research Update Genome Analysis

A substantial fraction of hypothetical open reading frames (ORFs) in completely sequenced bacterial genomes are short, suggesting that many are not genes but random stretches of DNA. Although it is not feasible to authenticate the coding capacity of all such regions experimentally, comparisons of ORFs in related genomes can expose those that encode functional proteins. The density of genes, coupled with the presence of several gene-specific features and the lack of introns, makes the identification of coding sequences in bacterial genomes a relatively straightforward procedure, at least whe