Cited by 32DNA and Biological ComputingAlgorithms and Data CompressionGenomics and Phylogenetic Studies

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

Open access
Xie, Ranze, Zan, Xiangzhen, Chu, Ling, Su, Yanqing, Xu, Peng, Liu, Wenbin·2023·BMC Bioinformatics

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.

AI snapshot

Written from the paper’s full text.

TL;DR

This paper simulates the error-correction capability of the MSA algorithm MAFFT for DNA storage and finds a phase transition at about 20% errors. Below this limit, MAFFT can approach complete recovery with sufficient sequencing depth; above it, performance plateaus poorly.

Key findings

  • MAFFT’s recovery accuracy shows a phase transition at roughly 20% errors: below this critical value, increasing sequencing depth can improve recovery; above it, recovery accuracy drops steeply and increasing depth does not help.
  • In the low error regime (p ≤ 8%), MAFFT can completely recover data; at p = 8%, it needs only 70 reads. In the medium regime (8% < p ≤ 15%), it can correct more than 90% of errors with sequencing depth ≤ 100.
  • At 13% error, increasing accuracy from 90% to 95% requires sequencing depth rising from 30 to 35, while improving from 95% to 99% requires 35 to 60 reads.
  • MAFFT is robust to imperfect clustering: with cluster accuracy as low as 0.6, average recovery accuracy remained greater than 0.95 at 10%, 12%, and 14% error rates. On a real nanopore dataset, MAFFT completely recovered about 92% of sequences at sequencing depth 20.

Methods

  • Simulation study: a text file (“The Grandmother”) was encoded with quaternary mapping (00-A, 01-T, 10-G, 11-C) into 140 DNA sequences of 120 bases (8 bases index, 112 bases data). Error rate p ranged from 1% to 40%, sequencing depth up to 4000, with average results from 100 repeated experiments.
  • MAFFT (FFT-NS-2) was used as the MSA algorithm; IDS errors were assumed uniformly random, and all reads were assumed correctly clustered in the main simulation.
  • Real dataset test used a Microsoft nanopore dataset with 10,000 DNA sequences of length 110 and 269,709 noisy nanopore reads; estimated insertion, deletion, and substitution rates were about 1.7%, 2%, and 2.2%, respectively. Recovery was assessed by average recovery accuracy and normalized Hamming distance.

Limitations

  • The paper states that simulation assumes all reads are clustered correctly and that IDS errors are uniformly random; in reality, error location and type are influenced by GC content, homopolymers, and reserved subsequences.
  • The paper notes that if a base is deleted in all reads, MSA alone cannot recover it, and that homopolymers cause more trouble for MSA.
  • The study uses MAFFT as a proof-of-concept for MSA generally; the authors believe results largely apply to other MSA algorithms, but this is not directly tested.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1186/s12859-023-05237-9

Cites

30 of 30 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 14 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    A significant portion of errors remain synchronization errors even with increased sequencing depth.

    “We observe that a significant portion of errors are still synchronization errors even with increased sequencing depth.”
    Quote in the paperSubstantial claim
  • Findingown data

    MAFFT's error correction capability exhibits a phase transition at around 20% errors.

    “Our results reveal that its capability exhibits a phase transition when there are around 20% errors.”
    • Also stated in: § The phase transition of the error correction capability · hedged
      “Results indicate that MAFFT's error correction capability exhibits a phase transition. Figure 1 shows two phase transitions of the average recovery accuracy at two I:D:S ratios (1:1:1(a) and 1:1:2(b)), and the critical value is at about 20% error.”
    • Also stated in: § Conclusion · hedged
      “Our simulation results indicate that its error correction limit is about 20% errors.”
    Quote in the paperSubstantial claim
  • Findingown data

    The average recovery accuracy at I:D:S ratio 1:1:1 is lower than that at I:D:S ratio 1:1:2.

    “Under the same conditions in Fig. 1a, b, we can see that the average recovery accuracy at I:D:S ratio 1:1:1 is lower than that of I:D:S ratio 1:1:2.”
    Quote in the paperSubstantial claim
  • Findingown data

    Below the critical error rate of about 20%, increasing sequencing depth can eventually allow MAFFT to approach complete recovery.

    “Below this critical value, increasing sequencing depth can eventually allow it to approach complete recovery.”
    • Also stated in: § The phase transition of the error correction capability · hedged
      “When the error rate is less than the critical value, increasing sequencing depth may improve the average recovery rate (see the lower red region in Fig. 1).”
    Quote in the paperSubstantial claim
  • Findingown data

    In the medium error regime, the needed sequencing depth to reach higher accuracy increases dramatically at a given error rate.

    “The various curves in Fig. 2b show that, at a given error rate, the needed sequencing depth to reach higher accuracy increases dramatically.”
    Quote in the paperSubstantial claim
  • May combine two claims. 21
  • Classified as probably not a substantial claim. 11
  • May combine two claims.

    Findingown data

    Above the critical error rate of about 20%, MAFFT's recovery accuracy drops steeply to less than 50% in most cases and increasing sequencing depth cannot improve it.

    “Otherwise, its performance plateaus at some poor levels.”
    • Also stated in: § The phase transition of the error correction capability · plain
      “On the contrary, the recovery accuracy drops steeply to even less than 50% in most cases when the error rate is larger than the critical value. And increasing sequencing depth could not improve the recovery accuracy (see the upper blue region in Fig. 1).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    At error rate 13%, improving accuracy from 90% to 95% requires increasing sequencing depth from 30 to 35; improving from 95% to 99% requires increasing from 35 to 60.

    “For example, at error rate 13%, to improve the accuracy from 90 to 95%, the needed sequence only increases from 30 to 35. However, this number increases from 35 to 60 in order to improve the accuracy from 95 to 99%.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingreasoning

    MSA can handle 99% and 95% of the errors at p = 12% and 14%, respectively, with needed sequencing depth about 50.

    “For example, we could let MSA handle 99% and 95% of the errors at p = 12% and 14%, where the needed sequencing depth is about 50.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingreasoning

    In the clustering accuracy experiment, average recovery accuracy slightly decreased when noisy reads were added, but remained greater than 0.95 even when clustering accuracy was as low as 0.6.

    “Although the average recovery accuracy slightly decreased when we added noisy reads, they are all still greater than 0.95 even when the clustering accuracy is as low as 0.6.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Most errors in the real dataset usually occur when there are homopolymers, which are highly prevalent in this dataset.

    “In addition, we find that most of these errors usually occur when there are homopolymers, such as the example in Fig. 4c, which are highly prevalent in this dataset.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    In the real dataset, one typical alignment error was caused by a deletion of base G in most reads, and another by misaligning some base C to the next position.

    “The first one is caused by a deletion of base ‘G’ in most reads. The second one is caused by misaligning some base C to the next position.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationnone given

    By selecting an appropriate sequencing depth, the MSA strategy can achieve an optimal trade-off between cost and reading speed.

    “Furthermore, by selecting an appropriate sequencing depth, this strategy could achieve an optimal trade-off between cost and reading speed.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: The main cost in DNA storage comes from synthesis.
    • Rests on an assumption: Retrieval efficiency is mainly determined by the average sequencing depth and decoding time complexity.
  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    MSA can be combined with other means such as ECC, repeated markers, or any other code constraints.

    “It could also be combined with other means such as ECC, repeated markers, or any other code constraints.”
    • Also stated in: § The error correction capability · hedged
      “Therefore, it would be a wise alternative to combine MSA with other means, such as markers, ECC, or constraints on encoding.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationreasoning

    If most errors are solved by MSA, added redundancy will be significantly reduced and a relatively high logical density approaching 2 bits/nt can still be achieved.

    “As most of these errors are solved by MSA, the added redundancy will be significantly reduced and thus still achieve a relatively high logical density approaching 2 bits/nt.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationreasoning

    Since simple quaternary encoding and constraints were used, MAFFT can achieve complete recovery with reasonably little copies and minimal loss in logical density.

    “Since we only used the simple quaternary encoding and constraints, this means that MAFFT can achieve complete recovery with reasonably little copies and minimal loss in logical density.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationown data

    The needed sequencing depth and logical redundancy of Yazdi et al.'s method could be further optimized.

    “From our results in Fig. 2b, the needed sequencing depth and logical redundancy of this method could be further optimized.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Premisecitation

    In the high error regime, the modulation-based method proposed by our group is perhaps the best solution today, as it could correct up to 40% errors.

    “In the high error regime, the modulation-based method proposed by our group is perhaps the best solution today, as it could correct up to 40% errors.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [19] Zan X, Xie R, Yao X, Xu P, Liu W. A robust and efficient DNA storage architecture based on modulation encoding and decoding. bioRxiv 2022. source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The post-alignment voting process can retain conserved information and filter out most noises, explaining robustness to imperfect clustering.

    “This may be explained by the post-alignment voting process’s ability to retain the conserved information and filter out most of the noises.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisenone given

    Both the error correction capability and logical density of the modulation-based method are superior to the method proposed by Lenz et al.

    “Both of its error correction capability and logical density are superior to the method proposed by Lenz et al. [16].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [16] Lenz A, Maarouf I, Welter L, Wachter-Zeh A, Amat A. Concatenated codes for recovery from multiple reads of DNA sequences. 2020.

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S4 (based). May combine two claims.

    Interpretationnone given

    MSA requires no redundancy, which is crucial for high logical density.

    “First, it requires no redundancy which is crucial for high logical density.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S4 (based). May combine two claims.

    Interpretationnone given

    MSA's decoding process is quasi-linear, which is beneficial for efficient information retrieval.

    “Second, its decoding process is quasi-linear which is beneficial for efficient information retrieval.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationreasoning

    A more accurate MSA algorithm, such as SATe, while slower, would most likely require less sequencing depth to achieve the same recovery rate as MAFFT.

    “A more accurate MSA algorithm, such as SATe, while slower, would most likely require less sequencing depth to achieve the same recovery rate as MAFFT.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationreasoning

    In the low error regime, MSA alongside the simplest encoding and constraints is perhaps the optimal choice: it achieves complete recovery with minimal loss in logical density while requiring only quasi-linear time complexity and modest sequencing depth.

    “In the low error regime, MSA alongside the simplest encoding and constraints is perhaps the optimal choice: it achieves complete recovery with minimal loss in logical density while requiring only quasi-linear time complexity and modest sequencing depth.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationreasoning

    MSA can solve most IDS errors using the simplest quaternary encoding (minimal loss of logical density) while requiring only modest sequencing depths.

    “The main advantage of MSA is that it can solve most of the IDS errors using the simplest quaternary encoding (minimal loss of logical density) while requiring only modest sequencing depths.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S2 (checkable), S4 (based).

    Interpretationnone given

    MSA can be combined with other means to provide a flexible architecture to design an MSA-dominated error correcting mechanism.

    “Lastly, it can be combined with other means to provide a flexible architecture to design a MSA-dominated error correcting mechanism.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationreasoning

    A more accurate MSA algorithm is unlikely to have a higher practical error correction limit, since sequencing depth in the thousands would be even more infeasible for accurate but slower algorithms.

    “It is also unlikely to have a higher practical error correction limit, since a sequencing depth in the thousands would be even more infeasible for these accurate but much slower algorithms.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    A base deletion in most reads is irrecoverable by MSA, while misalignment may be improved by increasing sequencing depth.

    “Obviously, the former could not be solved because a base deletion in most reads would be irrecoverable by MSA, while the latter may be improved by increasing sequencing depth.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    In the low error regime, MSA could accomplish complete recovery while retaining maximum logical density.

    “In the low error regime, MSA could accomplish complete recovery while retaining maximum logical density.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisecitation

    The error rate of second-generation synthesis and sequencing technology is less than 5%, while that of third-generation is about 10-15%.

    “The error rate of the second-generation synthesis and sequencing technology is less than 5%, while that of the third-generation is about 10–15% [31, 32].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [31] Lopez R, Chen Y-J, Dumas Ang S, Yekhanin S, Makarychev K, Racz MZ, Seelig G, Strauss K, Ceze L. DNA assembly for nanopore data storage readout. Nat Commun. 2019;10(1):2933. source

      Not checked in the free run.

    • cites [32] Jain M, Tyson JR, Loose M, Ip CLC, Eccles DA, O’Grady J, Malla S, Leggett RM, Wallerman O, Jansen HJ, et al. MinION analysis and reference consortium: phase 2 data release and analysis of R90 chemistry. F1000Res. 2017;6:760–760. source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    For each error rate and sequencing depth, the average results were obtained from 100 repeated experiments.

    “For each error rate and sequencing depth, the average results are obtained from 100 repeated experiments.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    By default, MAFFT chooses FFT-NS-2, the strategy optimized for speed, which is on par with the fastest MSA algorithms.

    “By default, it chooses FFT-NS-2, the strategy optimized for speed, which is on par with the fastest MSA algorithms [29].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [29] Pervez MT, Babar ME, Nadeem A, Aslam M, Awan AR, Aslam N, Hussain T, Naveed N, Qadri S, Waheed U, et al. Evaluating the accuracy and efficiency of multiple sequence alignment methods. Evolut Bioinform. 2014;10:19199. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    MAFFT also provides strategies that are state-of-the-art in terms of alignment accuracy, such as L-INS-i, which is comparable to the most accurate algorithms.

    “But it also provides strategies that are state-of-the-art in terms of alignment accuracy, such as L-INS-i [29], which is comparable to the most accurate algorithms.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [29] Pervez MT, Babar ME, Nadeem A, Aslam M, Awan AR, Aslam N, Hussain T, Naveed N, Qadri S, Waheed U, et al. Evaluating the accuracy and efficiency of multiple sequence alignment methods. Evolut Bioinform. 2014;10:19199. source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    MAFFT has good accuracy and takes only quasi-linear time for pairwise comparison.

    “MAFFT has good accuracy and takes only quasi-linear time for pairwise comparison.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [29] Pervez MT, Babar ME, Nadeem A, Aslam M, Awan AR, Aslam N, Hussain T, Naveed N, Qadri S, Waheed U, et al. Evaluating the accuracy and efficiency of multiple sequence alignment methods. Evolut Bioinform. 2014;10:19199. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    In the clustering accuracy experiment, average recovery accuracy at 10%, 12%, and 14% error rates was obtained after repeating the experiment 500 times.

    “Additionally, Fig. 3 shows the average recovery accuracy at 10%, 12%, and 14% error rates after repeating the experiment 500 times.”
    Quote in the paperNot a substantial claim
29 of 29
  • The authors state this as an assumption.

    The location and type of base errors introduced in synthesis and sequencing are random, so IDS errors are distributed uniformly at random.

    “While there are specific patterns where error occurrence is more likely, for simplicity, we assume the location and type of base errors introduced in synthesis and sequencing are random. Hence, the IDS errors are distributed uniformly at random.”
  • The authors state this as an assumption.

    All reads have been clustered correctly.

    “For simulation experiments, we assume that all reads have been clustered correctly and we focus on the reconstruction problem of these clustered sequences using MAFFT.”
  • The authors state this as an assumption.

    A successful synthesis is assumed when considering the effect of indels on the synchronization problem.

    “This is coincident with our intuition that assuming a successful synthesis, the more insertions/deletions (indels) in the sequenced reads, the harder it is to solve the synchronization problem.”
  • The paper relies on this without support.

    Homopolymers tend to introduce more IDS errors.

    “It is well-known that homopolymers tend to introduce more IDS errors.”
  • The paper relies on this without support.

    The location and type of errors are not purely random, as they can be influenced by various error sources (GC content, homopolymers, reserved subsequences).

    “Furthermore, the location and type of errors are not purely random, as they can be influenced by various error sources (GC content, homopolymers, reserved subsequences).”
  • The paper relies on this without support.

    A base deletion in all reads has a non-negligible probability of occurring during synthesis.

    “The downside is that if a base was deleted in all the reads, which does have a non-negligible probability of occurring during synthesis, MSA alone has no way to recover it.”
  • The paper relies on this without support.

    MSA is a parameter-free error correction method whose performance is determined by the sequence copies used (or sequencing depth).

    “MSA is a parameter-free error correction method whose performance is determined by the sequence copies used (or sequencing depth).”
  • The paper relies on this without support.

    The main cost in DNA storage comes from synthesis.

    “The main cost in DNA storage comes from synthesis.”
  • The paper relies on this without support.

    Retrieval efficiency is mainly determined by the average sequencing depth and decoding time complexity.

    “On the other hand, retrieval efficiency is mainly determined by the average sequencing depth and decoding time complexity.”
9 of 9

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Adequately deep sequencing combined with MSA is able to correct errors when their frequency is less than 20%; above this value, error correction based on MSA is possible with simultaneous use of ECC.

    “The authors showed that adequately deep sequencing combined with MSA is able to correct errors when their frequency is less than 20%. Above this value, error correction based on MSA is possible with the simultaneous use of ECC.”

    From DNA Data Storage. (2023) · cites this paper as [34]

    The Results section, “The phase transition of the error correction capability” (page unavailable), says that below about 20% errors, greater sequencing depth can improve recovery. It also says that above this threshold MSA cannot capture useful information; the paper proposes combining MSA with ECC for the medium error regime, with examples at 12% and 14%, not for errors above 20%. (LLM, conf=0.88)

    Experimental — accuracy not yet measured
  • Xie et al. (2023) showed that the MAFFT algorithm can correct more than 95% of errors at a sequencing depth reaching 100× when the error rate is lower than 15%.

    “The MAFFT algorithm was chosen for the analysis, which has been shown to be able to correct more than 95% of errors at a sequencing depth reaching 100× when the error rate is lower than 15%.”

    From DNA Data Storage. (2023) · cites this paper as [34]

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. Morrison DA. Multiple sequence alignment is not a solved problem. arXiv 2018.

Cited by

Sorted by citations

Authors
Xie, R., Zan, X., Chu, L., Su, Y., Xu, P., & Liu, W.
Affiliations
Guangzhou University (CN)
Corresponding author
  • Xu, Peng
  • Liu, Wenbin
Venue
BMC Bioinformatics
Published
2023-03-23
Volume
24
Issue
1
Pages
111-111
ISSN
1471-2105 (ISSN-L)
OpenAlex
W4360611676
Cited by
32
References
30
Citations by year
2026: 9 · 2025: 7 · 2024: 12 · 2023: 4
FWCI
2.85
Type
journal article
Language
en
Open access
Locations
  • BMC Bioinformatics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
National Natural Science Foundation of China (62002079, 62072128)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
  • Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
DNA data storage, multiple sequence alignment, MAFFT, error correction, synchronization error, indels, sequencing depth, phase transitions, error recovery, error-correcting codes
MeSH terms
Algorithms, Computer Simulation, DNA, Sequence Alignment, Sequence Analysis, DNA

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