Collaborative Research: CIF: Small: Coded String Reconstruction Problems in Molecular Storage

合作研究：CIF：小型：分子存储中的编码串重建问题

• 批准号: 2007238
• 负责人: Wojciech Szpankowski
• 金额: $ 25万
• 依托单位: Purdue University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-10-01 至 2024-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2007238&HistoricalAwards=false
• 关键词: Collaborative; Research; CIF; Small; Coded

The problem of reconstructing text strings from their fragments or masses of fragments is of focal importance in computational biology as current DNA and protein sequencing platforms are unable to read the content of long strings that denote protein/gene sequences. One prototypical example of string reconstruction arises in DNA assembly: there, one creates multiple copies of the same long string and cuts the copies to read out short overlapping substrings that can be put together by matching their prefixes and suffixes. The reconstructed string may not be a perfect replica of the original string due to errors in the fragmentation and matching processes. Furthermore, for many strings unique reconstruction is inherently impossible. This represents a major issue for next generation sequencing technologies used in fundamental biological research, since in this setting it is impossible to ensure unambiguous results. The successful code designs pursued in this project can resolve reliability and content retrieval issues impeding implementations of emerging molecular computing and storage paradigms. This project is concerned with developing novel coding methods for unique reconstruction of strings or pools of strings based on their constituent substrings, subsequences and substring compositions. The techniques employed represent a combination of new graph-theoretic, combinatorial optimization and information theory approaches. In particular, the project will investigate the use of balanced partial de Bruijn strings for substring-based reconstruction, Catalan-like paths for multiset composition reconstruction as well as coded multi-trace reconstruction methods involving specialized modifications of deletion-correcting codes and superposition codes. The coding schemes will be tested on DNA-based and synthetic polymer-based data storage platforms under the development at the University of Illinois.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

从它们的片段或大量片段重建文本串的问题在计算生物学中具有焦点重要性，因为当前的DNA和蛋白质测序平台无法读取表示蛋白质/基因序列的长串的内容。一个典型的字符串重构的例子出现在DNA组装中：在那里，一个人创建了同一个长字符串的多个副本，并切割副本以读出短的重叠子串，这些子串可以通过匹配它们的前缀和后缀放在一起。由于分段和匹配过程中的错误，重建的字符串可能不是原始字符串的完美副本。此外，对于许多字符串来说，唯一的重构本质上是不可能的。这代表了基础生物学研究中使用的下一代测序技术的一个主要问题，因为在这种情况下，不可能确保明确的结果。在这个项目中追求的成功的代码设计可以解决阻碍新兴分子计算和存储范例实现的可靠性和内容检索问题。这个项目关注的是开发新的编码方法，用于基于其组成子串、连续性和子串组成来唯一地重建串或串池。所采用的技术代表了新的图论，组合优化和信息理论方法的组合。特别是，该项目将研究使用平衡的部分de Bruijn字符串进行基于子串的重建，用于多集组合重建的Catalan类路径以及涉及删除校正码和叠加码的专门修改的编码多迹重建方法。编码方案将在伊利诺伊大学开发的基于DNA和合成聚合物的数据存储平台上进行测试。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。