Suffixes Of String Research Articles

Engineering burstsort

Burstsort is a trie-based string sorting algorithm that distributes strings into small buckets whose contents are then sorted in cache. This approach has earlier been demonstrated to be efficient on modern cache-based processors [Sinha & Zobel, JEA 2004]. In this article, we introduce improvements that reduce by a significant margin the memory requirement of Burstsort: It is now less than 1% greater than an in-place algorithm. These techniques can be applied to existing variants of Burstsort, as well as other string algorithms such as for string management. We redesigned the buckets, introducing sub-buckets and an index structure for them, which resulted in an order-of-magnitude space reduction. We also show the practicality of moving some fields from the trie nodes to the insertion point (for the next string pointer) in the bucket; this technique reduces memory usage of the trie nodes by one-third. Importantly, the trade-off for the reduction in memory use is only a very slight increase in the running time of Burstsort on real-world string collections. In addition, during the bucket-sorting phase, the string suffixes are copied to a small buffer to improve their spatial locality, lowering the running time of Burstsort by up to 30%. These memory usage enhancements have enabled the copy-based approach [Sinha et al., JEA 2006] to also reduce the memory usage with negligible impact on speed.

An incomplex algorithm for fast suffix array construction

AbstractThe suffix array of a string is a permutation of all starting positions of the string's suffixes that are lexicographically sorted. We present a practical algorithm for suffix array construction that consists of two easy‐to‐implement components. First it sorts the suffixes with respect to a fixed length prefix; then it refines each bucket of suffixes sharing the same prefix using the order of already sorted suffixes. Other suffix array construction algorithms follow more complex strategies. Moreover, we achieve a very fast construction for common strings as well as for worst case strings by enhancing our algorithm with further techniques. Copyright © 2006 John Wiley & Sons, Ltd.

An efficient algorithm for the All Pairs Suffix-Prefix Problem

For a pair of strings ( S 1, S 2), define the suffix-prefix match of ( S 1, S 2) to be the longest suffix of string S 1 that matches a prefix of string S 2. The following problem is considered in this paper. Given a collection of strings S 1, S 2,..., S k of total length m, find the suffix-prefix match for each of the k( k − 1) ordered pairs of strings. We present an algorithm that solves the problem in O( m + k 2) time, for any fixed alphabet. Since the size of the input is Ω(m) and the size of the output is Ω(k 2) this solution is optimal.