ArticleBMC bioinformatics2023
Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Characterization of a novel Iflavirus from the locust Calliptamus italicus in Xinjiang, China.Virus genes · 2026Article
- A modulation-based encryption framework integrating channel and artificial noise for DNA storage.iScience · 2026Article
- Highly biased DNA sequence reconstruction in DNA storage with multi-scale attention mechanism and contrast learning.Synthetic and systems biotechnology · 2026Article
- Comparison of state-of-the-art error-correction coding for sequence-based DNA data storage.Nature communications · 2026Article
- DNA diamond formulates a decomposable composite letter constellation model for DNA data storage.Nature communications · 2026Article
- DVOUG enables robust DNA sequence assembly and reconstruction with a dynamic, variable-order graph.Cell reports methods · 2025Article
- Efficient trace reconstruction in DNA storage systems using bidirectional beam search.iScience · 2025Article
- Predict the degree of secondary structures of the encoding sequences in DNA storage by deep learning model.Scientific reports · 2025Article
- A generative adversarial network for multiple reads reconstruction in DNA storage.Scientific reports · 2024Article
- Recent progress in DNA data storage based on high-throughput DNA synthesis.Biomedical engineering letters · 2024Review
- Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review.Foods (Basel, Switzerland) · 2024Review
- Article
- DNA Bloom Filter enables anti-contamination and file version control for DNA-based data storage.Briefings in bioinformatics · 2024Article
- DNA Data Storage.Biotech (Basel (Switzerland)) · 2023Review
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6 authors.
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Abstract
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.
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