Reconstructing Mixtures of Coded Strings from Prefix and Suffix Compositions

Abstract

The problem of string reconstruction from substring information has found many applications due to its relevance in DNA-and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of strings based on the union of compositions of their prefixes and suffixes, generated by mass spectrometry readouts. We describe new coding methods that allow for unique joint reconstruction of subsets of strings selected from a code and provide matching upper and lower bounds on the asymptotic rate of the underlying codebooks. Under certain mild constraints on the problem parameters, one can show that the largest possible rate of a codebook that allows for all subcollections of ď h codestrings to be uniquely reconstructable from the prefix-suffix information equals 1{h.Index Terms-B h sequences, polymer-based data storage, unique string reconstruction.