Starts of bacterial genes: estimating the reliability of computer predictions

Exact mapping of gene starts is an important problem in the computer-assist ed functional analysis of newly sequenced prokaryotic genomes. We describe an algorithm for finding ribosomal binding sites without a learning sample. This algorithm is particularly useful for analysis of genomes with little or no experimentally mapped genes. There is a clear correlation between the ribosomal binding site (RBS) properties of a given genome and the potentia l gene start prediction accuracy. This correlation is of considerable predi ctive power and may be useful for estimating the expected success of future genome analysis efforts. We also demonstrate that the RES properties depen d on the phylogenetic position of a genome. (C) 1999 Elsevier Science B.V. All rights reserved.