The ribosome as a table-driven convolutional decoder for the Escherichia coli K-12 translation initiation system

Redundancy occurs naturally within RNA and DNA sequences. The existence of tandem repeats, and sequences such as the Shine-Dalgarno sequence, the Pribnow box and the TATA box, leads the authors to believe that cellular communication systems use some method of coding to recognize valid information regions within a nucleotide sequence and correct for "transmission" errors such as mutations. Here, the authors use principles of convolutional coding theory to analyse the translation initiation process. The principle hypothesis is that the messenger RNA (mRNA) sequence can be viewed as a noisy, convolutionary encoded signal. The ribosome is functionally paralleled to a table-driven convolutional decoder. The 16s ribosomal RNA (rRNA) sequence is used to form decoding masks for table-driven decoding. The results of applying this method to Escherichia coli K-12 strain MG1655 are presented.