The suffix tree is a very important data structure in string processing, but it suffers from a huge space consumption. In large-scale applications, compressed suffix trees (CSTs) are therefore used instead. A CST consists of three (compressed) components: the suffix array, the LCP-array, and data structures for simulating navigational operations on the suffix tree. The LCP-array stores the leng...

We study the problem of finding all k-periods of a length-n string S, presented as a data stream. S is said to have k-period p if its prefix of length n− p differs from its suffix of length n− p in at most k locations. We give a one-pass streaming algorithm that computes the k-periods of a string S using poly(k, logn) bits of space, for k-periods of length at most n 2 . We also present a two-pa...

Because of the increase in the size of genome sequence databases, the importance of indexing the sequences for fast queries grows. Suffix trees and suffix arrays are used for simple queries. However these are not suitable for complicated queries from huge amount of sequences because the indices are stored in disk which has slow access speed. We propose storing the indices in memory in a compres...

UNLABELLED Suffix tree is one of the most fundamental data structures in string algorithms and biological sequence analysis. Unfortunately, when it comes to implementing those algorithms and applying them to real genomic sequences, often the main memory size becomes the bottleneck. This is easily explained by the fact that while a DNA sequence of length n from alphabet sigma = {A, C, G, T} can ...

Lossless compression algorithms of the Lempel-Ziv (LZ) family are widely used nowadays. Regarding time and memory requirements, LZ encoding is much more demanding than decoding. In order to speed up the encoding process, efficient data structures, like suffix trees, have been used. In this paper, we explore the use of suffix arrays to hold the dictionary of the LZ encoder, and propose an algori...

A visual object can be conceived of as comprising a number of features bound together by their joint spatial location. We investigate the question of whether the spatial location is automatically bound to the features or whether the two are separable, using a previously developed paradigm whereby memory is disrupted by a visual suffix. Participants were shown a sample array of four colored shap...

In this paper a new permutation generator is proposed. Each subsequent permutation is generated in a cellular permutation network by reversing a suffix/prefix of the preceding permutation. The sequence of suffix/prefix sizes is computed by a complex parallel counter in O(1) time per generated object. Suffix/prefix reversing operations are performed at the same time when the permutation is actua...