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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Explorer: efficient DNA coding by De Bruijn graph toward arbitrary local and global biochemical constraints.

Chang Dou1, Yijie Yang1, Fei Zhu1

  • 1Center for Applied Mathematics, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China.

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New DNA data storage algorithms, Explorer and Codeformer, enhance encoding efficiency and decoding speed. These innovations address biochemical constraints, paving the way for practical DNA information storage solutions.

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Area of Science:

  • Bioinformatics
  • Data Storage Technologies
  • Molecular Engineering

Background:

  • Exponential growth in digital data necessitates novel storage solutions.
  • DNA offers high stability, density, and capacity for information storage.
  • Challenges include biochemical constraints and encoding/decoding efficiency.

Purpose of the Study:

  • To present Explorer, a high-efficiency DNA coding algorithm.
  • To introduce Codeformer, a fast transformer-based DNA decoding algorithm.
  • To evaluate the performance of these algorithms under various constraints.

Main Methods:

  • Explorer algorithm based on De Bruijn graphs for local sequence characterization.
  • Explorer's ability to handle homopolymers, GC content, and undesired motifs.
  • Codeformer algorithm utilizing transformer architecture for efficient decoding.

Main Results:

  • Explorer achieves stable encoding/decoding and increases encoding efficiency by ~10%.
  • Codeformer decoding efficiency exceeds traditional methods by over two-fold.
  • Combined Codeformer and Reed-Solomon code achieve >99% decoding accuracy.

Conclusions:

  • Explorer and Codeformer offer robust and efficient solutions for DNA data storage.
  • These algorithms overcome key biochemical and efficiency challenges in DNA storage.
  • Advancements support the development of practical DNA-based information storage systems.