Optimal generators for a systematic block code model of prokaryotic translation initiation

The decoding of received error control encoded bit streams is fairly straightforward when the channel encoding algorithms are efficient and known. But if the encoding scheme is unknown or part of the data is missing, how would one design a viable decoder for the received transmission? Communication engineers may not frequently encounter this situation, but for computational biologists this is an immediate challenge as we attempt to decipher and understand the vast amount of sequence data produced by genome sequencing projects. Assuming the systematic parity check block code model of protein translation initiation, this work presents an approach for determining the generator matrix given a set of potential codewords. The resulting generators and corresponding parity matrices are applied to valid and invalid Escherichia coli K-12 MG1655 messenger RNA leader sequences. The generators constructed using strict subsets of the 16S ribosomal RNA performed better than those constructed using the block code model in earlier works.