可扩展的正交 DNA 条形码库设计。

IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Nature computational science Pub Date : 2024-06-07 DOI:10.1038/s43588-024-00646-z
Gokul Gowri, Kuanwei Sheng, Peng Yin
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引用次数: 0

摘要

正交 DNA 条形码文库设计是生物工程中的一项重要任务。在此,我们介绍一种高效的条形码文库设计方法 Seqwalk,该方法满足序列对称性最小化(SSM)启发式正交性要求,理论上保证了在特定设计约束条件下最大或接近最大的文库规模。Seqwalk 将 SSM 约束条件编码为序列空间的 de Bruijn 图表示法,从而将离散数学1 的最新进展应用于正交序列设计问题。我们在一台标准笔记本电脑上用不到 20 秒的时间就设计出了大于 106 个满足 SSM 的条形码序列库,证明了 seqwalk 的可扩展性。
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Scalable design of orthogonal DNA barcode libraries
Orthogonal DNA barcode library design is an essential task in bioengineering. Here we present seqwalk, an efficient method for designing barcode libraries that satisfy a sequence symmetry minimization (SSM) heuristic for orthogonality, with theoretical guarantees of maximal or near-maximal library size under certain design constraints. Seqwalk encodes SSM constraints in a de Bruijn graph representation of sequence space, enabling the application of recent advances in discrete mathematics1 to the problem of orthogonal sequence design. We demonstrate the scalability of seqwalk by designing a library of >106 SSM-satisfying barcode sequences in less than 20 s on a standard laptop. Seqwalk is a scalable method for designing orthogonal DNA barcode libraries, producing one million barcodes in 20 s on a standard laptop.
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