Genomic position analyses and the transcription machinery.

Position analyses have been devised to extract additional transcriptional information from rapidly expanding genomic data bases. The locations of promoter regulatory sites and also the locations of transcription factor DNA-binding domains are analyzed. Strongly preferred positions of activator binding sites occur in both Escherichia coli and eukaryotes, suggesting specific common features of transcription in the two systems. In both systems, regulatory proteins are found to have their DNA-binding domains near termini and the data suggest an evolutionary analysis that complements a phylogenetic analysis based on sequence alignments. The results indicate that positional information can be an important adjunct to sequence comparisons in analyzing genomic information.