More Time-Space Tradeoffs for Finding a Shortest Unique Substring

• Published in: Algorithms Vol. 13; no. 9; p. 234
• Main Authors: Bannai, Hideo, Gagie, Travis, Hoppenworth, Gary, Puglisi, Simon J., Russo, Luís M. S.
• Format: Journal Article
• Language: English
• Published: MDPI AG 01.09.2020
• Subjects: k-mismatch SUS; Karp–Rabin; shortest unique substring; sketching; suffix trees; time-space tradeoff
• ISSN: 1999-4893; 1999-4893
• DOI: 10.3390/a13090234

We extend recent results regarding finding shortest unique substrings (SUSs) to obtain new time-space tradeoffs for this problem and the generalization of finding k-mismatch SUSs. Our new results include the first algorithm for finding a k-mismatch SUS in sublinear space, which we obtain by extending an algorithm by Senanayaka (2019) and combining it with a result on sketching by Gawrychowski and Starikovskaya (2019). We first describe how, given a text T of length n and m words of workspace, with high probability we can find an SUS of length L in O(n(L/m)logL) time using random access to T, or in O(n(L/m)log2(L)loglogσ) time using O((L/m)log2L) sequential passes over T. We then describe how, for constant k, with high probability, we can find a k-mismatch SUS in O(n1+ϵL/m) time using O(nϵL/m) sequential passes over T, again using only m words of workspace. Finally, we also describe a deterministic algorithm that takes O(nτlogσlogn) time to find an SUS using O(n/τ) words of workspace, where τ is a parameter.