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Related Experiment Video

Updated: Jan 10, 2026

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Published on: September 3, 2009

Efficient trace reconstruction in DNA storage systems using bidirectional beam search.

Zhenhao Gu^1,2, Hongyi Xin³, Puru Sharma¹

¹Department of Computer Science, School of Computing, National University of Singapore, Singapore 117417, Singapore.

|November 24, 2025

Summary

This summary is machine-generated.

We developed a new algorithm for DNA data storage that reconstructs sequences faster and more accurately. This bidirectional beam search (BBS) method improves DNA data storage efficiency and reliability.

Keywords:

biocomputational method computing methodology data storage representation signal reconstruction

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Area of Science:

Bioinformatics
Computational Biology
Data Storage

Background:

DNA data storage is a rapidly growing field requiring efficient decoding algorithms.
Current methods for trace reconstruction often use alignment or read correction, which have limitations in speed and generalizability.
These existing methods struggle with complex datasets and fixed error rate assumptions.

Purpose of the Study:

To develop a novel, efficient, and accurate algorithm for trace reconstruction in DNA data storage.
To address the limitations of existing methods by introducing a probabilistic approach.
To improve the speed and reliability of decoding data from noisy DNA sequences.

Main Methods:

A probabilistic formulation of trace reconstruction using a k-th order Markov chain model.
Identifying the consensus sequence most likely generated by the Markov chain.
Development of the bidirectional beam search (BBS) algorithm for linear-time consensus reconstruction.

Main Results:

The bidirectional beam search (BBS) algorithm reconstructs consensus sequences in linear time.
BBS achieves top-tier accuracy on multiple public Nanopore sequencing datasets.
BBS is approximately 20x faster than existing trace reconstruction methods.

Conclusions:

The proposed probabilistic approach and BBS algorithm significantly enhance DNA data storage efficiency.
BBS offers a more generalizable and faster solution for decoding noisy DNA sequencing reads.
This work has the potential to advance the practical application of DNA data storage systems.