An Algorithm for Suffix Sorting and Its Applications∗

The suffix tree is a data structure that has found applications in various important problems, such as genetic sequencing, pattern matching and computational biology. Its derivative data structure, the suffix array, is another representation with the added advantage of a small memory footprint. We propose a simple O(n log n) time divideand-conquer sort-and-merge algorithm for solving the suffix sorting problem. Given the suffix array, the array of Longest Common Prefix (LCP) can be constructed in O(n) time. Our proposed algorithm distinguishes itself from existing suffix array algorithms by the use of a relatively simple partitioning scheme at the division stage. We discuss applications suffix sorting to different problems in computational biology.