Is a genome a codeword of an error-correcting code?

• Published in: PloS one Vol. 7; no. 5; p. e36644
• Main Authors: Faria, Luzinete C B, Rocha, Andréa S L, Kleinschmidt, João H, Silva-Filho, Márcio C, Bim, Edson, Herai, Roberto H, Yamagishi, Michel E B, Palazzo, Jr, Reginaldo
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 23.05.2012; Public Library of Science (PLoS)
• Subjects: Algorithms; Applied mathematics; Base Sequence - genetics; Biology; Block codes; Codes; Coding theory; Computer Science; Deoxyribonucleic acid; Digital transmission; DNA; DNA Repair - genetics; DNA sequencing; Engineering; Error correcting codes; Error correction; Error correction & detection; Gene sequencing; Genes; Genome - genetics; Genomes; Genomics; Hamming codes; Lactococcus lactis - genetics; Linear algebra; Linear codes; Mathematics; Medical research; Medicine; Models, Genetic; Nucleotide sequence; Reed-Solomon codes; Theory; California
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0036644

Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction.