Predicting antisense RNAs in the genomes of Escherichia coli and Salmonella typhimurium using promoter-search algorithm PlatProm.

A pattern recognition software PlatProm, which takes into consideration both sequence-specific and structure-specific features in the genetic environment of the promoter sites and identifies transcription start points with a very high accuracy was used to reveal potentially transcribed regions in the genomes of two bacterial species. Along with the expected promoters located upstream from coding sequences PlatProm identified several hundred of very similar signals in other intergenic regions and within coding sequences. Homologous genes of Escherichia coli and Salmonella typhimurium, containing potential promoters on the template strand are suggested as putative targets for regulations by antisense RNA-products (aRNAs).