Applying Techniques from Frame Synchronization for Biological Sequence Analysis

During the last years, the amount of genetic data available has increased rapidly which creates the demand for advanced techniques for their interpretation. In the following, we present an approach of applying communication theory for biological sequence analysis. We use an analogy to frame synchronization to gain more insights into transcription, the step of copying a gene into messenger RNA (mRNA). In continuous and packet data transmission, successful decoding of a transmitted data stream at the receiver side strongly depends on the choice of the sync word that indicates the beginning of the message and thus needs to be detected reliably. Analogously, biological sync words indicate the beginning of a gene, i.e. they mark the sequence in the DNA that needs to be copied during transcription. These biological sync words are the -35 promoter region and the -10 promoter region named after their approximate position before the gene. In digital data transmission, the sync word is selected from all possible patterns based on its autocorrelation behavior. Therefore, we use an adapted autocorrelation function to investigate the synchronization properties of the promoter regions revealing that the -35 region is an outstanding synchronization pattern. In contrast to that, the -10 region, though more important for transcription initiation, showed to have worse properties. However, when including sequence constraints imposed through the region´s importance for transcription, the -10 region showed to be among the best possible sequences, too. These facts imply that during evolution promoter sequences evolved in a way to optimize their synchronization properties.