Escherichia coli promoters. II. A spacing class-dependent promoter search protocol

A computer search protocol for finding Escherichia coli bacterial and phage promoters is presented. This protocol relies heavily on the description of promoter sites developed in the preceding paper (O'Neill, M. C. (1989) J. Biol. Chem. 264, 5522-5530), with particular emphasis on the existence of a distinct consensus sequence for each of the three major spacing classes. The input sequence is tested independently for promoters with 16, 17, or 18 bases separating the -35 and -10 regions. Within a given spacing group, a series of six tests is employed to define possible promoters. These tests were developed empirically to identify members of the known promoter database with high efficiency while producing a minimal level of false positives. The degree to which this aim is met is discussed in the context of searches of random sequence, of pBR322, and of lambda.