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 selec...

• Type: Conference
• Year: 2007
• Where: ICC
• Authors: Johanna Weindl, Joachim Hagenauer
• Keywords: Biological Sync Words, Communications, ICC 2007, Promoter Regions, Sync Word