Is a Genome a Codeword of an Error-Correcting Code?

Abstract

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.

To Evolve or Not to Evolve? That is the Question

“…One of the simplest error detection and correction codes is the Hamming code such as the Hamming (7.4) code which can correct a single-bit error but detect one-bit and two-bit errors. It has been suggested that exon-intron genes are Hamming codewords (Faria et al, 2012). There are two main types of EDAC other than turbo codes -block codes and convolutional codes.…”

A novel approach for constructing reversible codes and applications to DNA codes over the ring F2[u]/(u<

“…The significance of this can be demonstrated as follows. In [8], Faria et al work on the ring Z 4 and they find a codeword that corresponds to a part of real DNA with one error. But, in doing so they do not fix a correspondence between elements of Z 4 and the DNA nucleotides.…”

Análise do splicing alternativo do Gene Hint-1 através do código BCH associado

“…O gene Hint-1 do nematoide C. elegans (identificado por "geneID"número 184760, no NCBI)é composto por 3éxons e 2íntrons com os seguintes comprimentos (em termos de nucleotídeos):éxon 1 com 123,íntron 1 com 44,éxon 2 com 138,íntron 2 com 74 eéxon 3 com 132, totalizando 511 nucleotídeos. Este gene foi identificado como uma palavra-código de um código BCH com parâmetros (511, 502, 3) sobre o anel Z 4 com polinômio gerador g(x) = x 9 + 2x 7 + x 5 + 3, via o algoritmo de geração de sequências de DNA proposto em [3]- [5]. A matriz geradora G tem dimensão 502 × 511.…”