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Current high-throughput sequencing technologies generate large numbers of relatively short and error-prone reads, making the de novo assembly problem challenging. Although high quality assemblies can be obtained by assembling multiple paired-end libraries with both short and long insert sizes, the latter are costly to generate. Recently, GAGE-B study showed… (More)

Motif finding is an important and a challenging problem in many biological applications such as discovering promoters, enhancers, locus control regions, transcription factors, and more. The (l, d)-planted motif search, PMS, is one of several variations of the problem. In this problem, there are n given sequences over alphabets of size [Formula: see text],… (More)

Approximate pattern matching is a fundamental problem in the bioinformatics and information retrieval applications. The problem involves different matching relations such as Hamming distance, edit distances, and the wildcards matching problem. The input is usually a text of length n over a fixed alphabet of length Σ, a pattern of length m, and an integer k.… (More)

Error Tree is a novel tree structure that is mainly oriented to solve the approximate pattern matching problems, Hamming and edit distances, as well as the wildcards matching problem. The input is a text of length n over a fixed alphabet of length Σ, a pattern of length m, and k. The output is to find all positions that have ≤ k Hamming distance, edit… (More)

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