Suffix trees and suffix arrays are the most prominent full-text indices, and their construction algorithms are well studied. In the literature, the fastest algorithm runs in O(n) time, while it requires O(n log n)-bit working space, where n denotes the length of the text. On the other hand, the most space-efficient algorithm requires O(n)-bit working space while it runs in O(n log n) time. It w...

We propose a sort-based algorithm for multiple sequence alignment using anchors. Anchors are determined by the use of suffix sorting along with position-based sorts. Potential anchor points are identified by a careful exploitation of the sorted suffixes obtained from a generalized suffix array of the input sequences. Final alignment is obtained by a recursive application of the suffix-sorting a...

We investigate whether suffix related features can significantly improve the performance of character-based approaches for Chinese word segmentation (CWS). Since suffixes are quite productive in forming new words, and OOV is the main error source for CWS, many researchers expect that suffix information can further improve the performance. With this belief, we tried several suffix related featur...

Suffix trees are by far the most important data structure in stringology, with myriads of applications in fields like bioinformatics, data compression and information retrieval. Classical representations of suffix trees require O(n log n) bits of space, for a string of size n. This is considerably more than the n log 2 σ bits needed for the string itself, where σ is the alphabet size. The size ...

Factor and suffix oracles have been introduced in [1] in order to provide an economic and efficient solution for storing all the factors and suffixes respectively of a given text. Whereas good estimations exist for the size of the factor/suffix oracle in the worst case, no average-case analysis has been done until now. In this paper, we give an estimation of the average size for the factor/suff...

Iowa State University 5.

Prediction suffix trees (PST) provide an effective tool for sequence modelling and prediction. Current prediction techniques for PSTs rely on exact matching between the suffix of the current sequence and the previously observed sequence. We present a provably correct algorithm for learning a PST with approximate suffix matching by relaxing the exact matching condition. We then present a self-bo...

Suffix tree construction algorithms based on suffix links are popular because they are simple to implement, can operate online in linear time, and because the suffix links are often convenient for pattern matching. We present an approach using edge-oriented suffix links, which reduces the number of branch lookup operations (known to be a bottleneck in construction time) with some additional tec...

The suffix tree is one of the most important data structures in string processing and comparative genomics. However, the space consumption of the suffix tree is a bottleneck in large scale applications such as genome analysis. In this article, we will overcome this obstacle. We will show how every algorithm that uses a suffix tree as data structure can systematically be replaced with an algorit...

A language L over an alphabet Σ is suffix-convex if, for any words x, y, z ∈ Σ∗, whenever z and xyz are in L, then so is yz. Suffixconvex languages include three special cases: left-ideal, suffix-closed, and suffix-free languages. We examine complexity properties of these three special classes of suffix-convex regular languages. In particular, we study the quotient/state complexity of boolean o...