Youngho Kim  Jeong Seop Sim

10.5626/JOK.2017.44.8.760

CUDA repetitive strings approximate string matching Parallel algorithm

Repetitive strings have been studied in diverse fields such as data compression, bioinformatics and so on. Recently, two problems of approximate periods of strings over integer alphabets were introduced, finding minimum δ-approximate periods and finding minimum γ-approximate periods. Both problems can be solved in O(n²) time when n is the length of the string. In this paper, we present two parallel algorithms for solving the above two problems in O(n²) time using O(n²) threads, respectively. The experimental results show that our parallel algorithms for finding minimum δ-approximate (resp. γ-approximate) periods run approximately 19.7 (resp. 40.08) times faster than the sequential algorithms when n = 10,000.