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Trace Reconstruction Problems in Computational Biology
arXiv - CS - Computational Complexity Pub Date : 2020-10-12 , DOI: arxiv-2010.06083
Vinnu Bhardwaj, Pavel A. Pevzner, Cyrus Rashtchian, Yana Safonova

The problem of reconstructing a string from its error-prone copies, the trace reconstruction problem, was introduced by Vladimir Levenshtein two decades ago. While there has been considerable theoretical work on trace reconstruction, practical solutions have only recently started to emerge in the context of two rapidly developing research areas: immunogenomics and DNA data storage. In immunogenomics, traces correspond to mutated copies of genes, with mutations generated naturally by the adaptive immune system. In DNA data storage, traces correspond to noisy copies of DNA molecules that encode digital data, with errors being artifacts of the data retrieval process. In this paper, we introduce several new trace generation models and open questions relevant to trace reconstruction for immunogenomics and DNA data storage, survey theoretical results on trace reconstruction, and highlight their connections to computational biology. Throughout, we discuss the applicability and shortcomings of known solutions and suggest future research directions.

中文翻译:

计算生物学中的痕迹重建问题

从容易出错的副本中重建字符串的问题,即轨迹重建问题,是由 Vladimir Levenshtein 在 20 年前提出的。虽然在痕迹重建方面已经有大量的理论工作,但在两个快速发展的研究领域:免疫基因组学和 DNA 数据存储的背景下,实用的解决方案直到最近才开始出现。在免疫基因组学中,痕迹对应于基因的突变拷贝,突变是由适应性免疫系统自然产生的。在 DNA 数据存储中,痕迹对应于编码数字数据的 DNA 分子的嘈杂副本,错误是数据检索过程的人工产物。在本文中,我们介绍了几个新的痕迹生成模型和与免疫基因组学和 DNA 数据存储的痕迹重建相关的开放问题,调查轨迹重建的理论结果,并强调它们与计算生物学的联系。在整个过程中,我们讨论了已知解决方案的适用性和缺点,并提出了未来的研究方向。
更新日期:2020-10-14
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