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...e at the heart of many efficient string processing algorithms [1,2,8,15]. Despite its utility, the problem of constructing LCPx efficiently has been little studied. The three algorithms that do exist =-=[9,12]-=- consume significant amounts of memory and, though asymptotically linear in their runtime, have poor locality ⋆ This work is supported by the Australian Research Council. S.-H. Hong, H. Nagamochi, and...

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...m for constructing the LCP-array in linear time. A few refinements of ∗Computer Science Department, Karlsruhe University, johannes.fischer@kit.edu 1 this algorithm led to improvements in either space =-=[16]-=- or in running time [10]. However, these algorithms could not compete with the carefully tuned algorithms for suffix arrays. This led to the odd situation that the rather difficult task of sorting suf...

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...China” is used in “History of China”, in the Basque version) leading to larger expected LCP values. We compute suffix arrays and LCP tables for all the texts, using Manzini and Ferragina’s algorithms =-=[19,18]-=- and implementation 5 . These algorithms are chosen for their low space-consumption properties. For each text, we calculate the values Lmax, Lave, Lperc as defined previously (see Sect. 3, page 8). We...

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...2, 21] and suffix array methods [22, 23], has greatly increased the efficiency of searching and storing strings. The analysis described here makes use of the suffix array [24], and the associated LCP =-=[25]-=- (Longest Common Prefix) array which require significantly less memory than suffix trees [26] but which can still be constructed in linear time [27, 28, 29]. One of the major difficulties in comprehen...

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...construction of the respective suffix tree. Other algorithms for constructing suffix arrays can be found in [17, 36, 47, 55, 68]. Moreover, a recent line of research concerns compressed suffix arrays =-=[46, 38, 39, 35]-=-. Concerning applications, the main weakness of the suffix array in comparison with the suffix tree data structure is that the range of application in which it can be used is limited. To resolve this ...

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... [16,14] are certainly much faster, as well as more space-efficient, in practice [18], in some cases requiring space only for x and SAx itself. Given x and SAx, LCPx can also be computed in Θ(n) time =-=[11,15]-=-: the first algorithm described in [15] requires 9n bytes of storage and is almost as fast in practice as that of [11], which requires 13n bytes. (For space calculations, we make throughout the usual ...

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...e commun entre deux suffixes consécutifs dans l’ordre lexicographique). Cependant, la construction d’une telle table n’est pas gratuite et nécessite 9mq octets en mémoire avec l’algorithme deManzini [=-=Manzini, 2004-=-]. Nous vous proposons deux versions desGk arrays : une qui indexe seulement les reads de longueur fixe, puis une autre qui s’occupe des reads avec des longueurs variables. Dans la suite des résultats...