Quantitative computer analysis of signal sequence homologies in DNA

Homologies to prokaryotic recognition sites for RNA polymerase, ribosomes, and cyclic-AMP receptor protein (CRP), are analyzed by a new computer program using weighting factors to account for the statistical variation at each position of the consensus. Known signal sequence sites are easily detected by this algorithm, and other sites with equally strong homology are found whose biological function is still unknown. Some sites are biologically active even though they have very weak homology. No arbitrary 'cutoff score' can distinguish active recognition sites from inactive homologies; experiments must determine why certain weak homologies are able to function while others are not.