Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage

• Published in: BMC bioinformatics Vol. 24; no. 1; pp. 111 - 11
• Main Authors: Xie, Ranze, Zan, Xiangzhen, Chu, Ling, Su, Yanqing, Xu, Peng, Liu, Wenbin
• Format: Journal Article
• Language: English
• Published: London BioMed Central 23.03.2023; BioMed Central Ltd; BMC
• Subjects: Accuracy; Algorithms; Alignment; Bioinformatics; Biomedical and Life Sciences; Clustering; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Computer Simulation; Conserved sequence; Deoxyribonucleic acid; DNA; DNA - genetics; DNA barcoding; DNA storage; Error correction; Error correction & detection; Error-correcting codes; Genomic libraries; Health aspects; Heuristic; Information processing; Information retrieval; Information storage; Life Sciences; MAFFT; Management; Methods; Microarrays; Multiple sequence alignment; Nucleotide sequence; Phase transitions; Plateaus; Recovery; Redundancy; Sequence Alignment; Sequence Analysis, DNA; Software; Synchronism; Synchronization; China; Error correction; MAFFT; DNA storage; Multiple sequence alignment
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-023-05237-9

Synchronization (insertions–deletions) errors are still a major challenge for reliable information retrieval in DNA storage. Unlike traditional error correction codes (ECC) that add redundancy in the stored information, multiple sequence alignment (MSA) solves this problem by searching the conserved subsequences. In this paper, we conduct a comprehensive simulation study on the error correction capability of a typical MSA algorithm, MAFFT. Our results reveal that its capability exhibits a phase transition when there are around 20% errors. Below this critical value, increasing sequencing depth can eventually allow it to approach complete recovery. Otherwise, its performance plateaus at some poor levels. Given a reasonable sequencing depth (≤ 70), MSA could achieve complete recovery in the low error regime, and effectively correct 90% of the errors in the medium error regime. In addition, MSA is robust to imperfect clustering. It could also be combined with other means such as ECC, repeated markers, or any other code constraints. Furthermore, by selecting an appropriate sequencing depth, this strategy could achieve an optimal trade-off between cost and reading speed. MSA could be a competitive alternative for future DNA storage.