Reconstruction From Noisy Substrings

Hengjia Wei, Moshe Schwartz, Gennian Ge

Research output: Contribution to journalArticlepeer-review

Abstract

This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This coded reconstruction problem has applications in DNA storage. We consider both single-strand reconstruction codes and multi-strand reconstruction codes, where the message is encoded into a single strand or a set of multiple strands, respectively. Various parameter regimes are studied. New codes are constructed, some of whose rates asymptotically attain the upper bounds.

Original languageEnglish
Pages (from-to)7757-7776
Number of pages20
JournalIEEE Transactions on Information Theory
Volume70
Issue number11
DOIs
StatePublished - 1 Jan 2024

Keywords

  • DNA storage
  • robust positioning sequences
  • sequence (string) reconstruction
  • substitution
  • substring-distant sequences

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Library and Information Sciences

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