Algorithms of self-synchronizing single-deletion-correcting codes

TL;DR

This paper introduces a novel self-synchronizing coding approach for DNA sequences that corrects single-deletion errors without delimiters, inspired by biological 'codes without commas' and based on complementary information set codes.

Contribution

It presents a new algorithm for single-deletion correction in continuous DNA transmissions using self-synchronizing codes without delimiters, enhancing transmission efficiency.

Findings

Developed encoding and decoding algorithms for self-synchronizing DNA codes.

Achieved correction of single-deletion errors without using delimiters.

Provided concrete examples demonstrating the algorithms' effectiveness.

Abstract

This study explores the self-synchronization problem in DNA coding, specifically addressing single-deletion errors without using delimiters between codewords. We aim to identify the beginning of each codeword without using delimiters, enhancing the transmission efficiency. The motivation arises from the inefficiency of adding meaningless symbols as delimiters, decreasing the information rate. In addition, the historical context in biology, specifically Francis Crick's proposal of ``codes without commas'' for DNA sequences, inspires this investigation. We introduce a novel approach for correcting single-deletion errors in continuous transmissions without delimiters, distinguishing the beginning and end of each codeword. This approach is based on the properties of {\it complementary information set codes}, which is used to present an algorithm for {\it single-deletion correcting codes} with self-synchronizing capability. Accordingly, we present encoding and decoding algorithms for self-synchronizing single-deletion correcting DNA codes with concrete examples.