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Suffix trees are by far the most important data structure in stringology, with a myriad of applications in fields like bioinformatics and information retrieval. Classical representations of suffix trees require &Theta;(<i>n</i> log <i>n</i>) bits of space, for a string of size <i>n</i>. This is considerably more than the <i>n</i> log<sub>2</sub> &sigma;(More)
BACKGROUND Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these techniques also raise important computational difficulties mostly due to the huge volume of data produced, but also because of some of their(More)
A compressed full-text self-index for a text T , of size u, is a data structure used to search patterns P , of size m, in T that requires reduced space, i.e. that depends on the empirical entropy (H k , H0) of T , and is, furthermore, able to reproduce any substring of T. In this paper we present a new compressed self-index able to locate the occurrences of(More)
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,(More)
—We present a new algorithm to calculate exact hy-pervolumes. Given a set of d-dimensional points, it computes the hypervolume of the dominated space. Determining this value is an important subroutine of Multiobjective Evolutionary Algorithms (MOEAs). We analyze the " Quick Hypervolume " (QHV) algorithm theoretically and experimentally. The theoretical(More)
Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2 -L(More)
We study parallel and distributed compressed indexes. Compressed indexes are a new and functional way to index text strings. They exploit the compressibility of the text, so that their size is a function of the compressed text size. Moreover, they support a considerable amount of functions, more than many classical indexes. We make use of this extended(More)