Alphabet-dependent Parallel Algorithm for Suffix Tree Construction for Pattern Searching
نویسندگان
چکیده
منابع مشابه
Alphabet-dependent Parallel Algorithm for Suffix Tree Construction for Pattern Searching
Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel algorithm which attempts to take advantage of the perverseness of the multicore architecture. Microsatellites are important for their biological relevance he...
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The suffix tree is a compacted trie of all suffixes of a given string. It is a fundamental data structure in a wide range of domains such as text processing, data compression, computer vision, computational biology, and so on [1]. Moreover, it can be used for network researches such as web analysis, which has been studied actively [2], [3]. For example, suffix trees have been utilized to effect...
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We present a simple linear work and space, and polylogarithmic time parallel algorithm for generating multiway Cartesian trees. As a special case, the algorithm can be used to generate suffix trees from suffix arrays on arbitrary alphabets in the same bounds. In conjunction with parallel suffix array algorithms, such as the skew algorithm, this gives a rather simple linear work parallel algorit...
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In this study, we present an online suffix tree construction approach where multiple sequences are indexed by a single suffix tree. Due to the poor memory locality and high space consumption, online suffix tree construction on disk is a striving process. Even more, performance of the construction suffers when alphabet size is large. In order to overcome these difficulties, first, we present a s...
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Large string datasets are common in a number of emerging text and biological database applications. Common queries over such datasets include both exact and approximate string matches. These queries can be evaluated very efficiently by using a suffix tree index on the string dataset. Although suffix trees can be constructed quickly in memory for small input datasets, constructing persistent tre...
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ژورنال
عنوان ژورنال: International Journal of Grid and Distributed Computing
سال: 2017
ISSN: 2005-4262,2005-4262
DOI: 10.14257/ijgdc.2017.10.1.02