We have made use of a new computer program which rapidly searches for DNA patterns irrespective of the exact sequence, in order to search systematically for repetitive palindromic structures on the Escherichia coli chromosome. By using a relatively restrictive criterion, we detected three families of palindromic structures. One is present in ribosomal RNA operons. Since seven identical ribosomal RNA operons are found on the E. coli genome, this constitutes a validation of the method. Another family is constituted by the extragenic palindromic units (PUs or REP) already described (Gilson et al., 1984). We propose a slightly different consensus for this highly repetitive and dispersed family. The last is a subclass of symmetrical transcription termination sites which we have identified. They are present in four attenuator sites and at least one terminator for convergent operons. We suggest that these symmetrical terminator sites may play a general role in the termination of transcription for convergent operons. We discuss briefly how this type of approach could be used to analyse the structure of genomes.

We describe a program that efficiently searches sequence data banks for complex patterns where sites are linked by common relations such as identity, complementarity or span. Its algorithm is closer to those of automatic demonstration than to the finite state machines used in fast pattern matching. The repertory of relations can be enriched at will without rewriting the core of the program. The program is written in Pascal-ISO and runs on a microcomputer.