18,591 research outputs found

    Faster Approximate String Matching for Short Patterns

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    We study the classical approximate string matching problem, that is, given strings PP and QQ and an error threshold kk, find all ending positions of substrings of QQ whose edit distance to PP is at most kk. Let PP and QQ have lengths mm and nn, respectively. On a standard unit-cost word RAM with word size wlognw \geq \log n we present an algorithm using time O(nkmin(log2mlogn,log2mlogww)+n) O(nk \cdot \min(\frac{\log^2 m}{\log n},\frac{\log^2 m\log w}{w}) + n) When PP is short, namely, m=2o(logn)m = 2^{o(\sqrt{\log n})} or m=2o(w/logw)m = 2^{o(\sqrt{w/\log w})} this improves the previously best known time bounds for the problem. The result is achieved using a novel implementation of the Landau-Vishkin algorithm based on tabulation and word-level parallelism.Comment: To appear in Theory of Computing System

    Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts

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    We study the approximate string matching and regular expression matching problem for the case when the text to be searched is compressed with the Ziv-Lempel adaptive dictionary compression schemes. We present a time-space trade-off that leads to algorithms improving the previously known complexities for both problems. In particular, we significantly improve the space bounds, which in practical applications are likely to be a bottleneck

    A practical index for approximate dictionary matching with few mismatches

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    Approximate dictionary matching is a classic string matching problem (checking if a query string occurs in a collection of strings) with applications in, e.g., spellchecking, online catalogs, geolocation, and web searchers. We present a surprisingly simple solution called a split index, which is based on the Dirichlet principle, for matching a keyword with few mismatches, and experimentally show that it offers competitive space-time tradeoffs. Our implementation in the C++ language is focused mostly on data compaction, which is beneficial for the search speed (e.g., by being cache friendly). We compare our solution with other algorithms and we show that it performs better for the Hamming distance. Query times in the order of 1 microsecond were reported for one mismatch for the dictionary size of a few megabytes on a medium-end PC. We also demonstrate that a basic compression technique consisting in qq-gram substitution can significantly reduce the index size (up to 50% of the input text size for the DNA), while still keeping the query time relatively low

    Prospects and limitations of full-text index structures in genome analysis

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    The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared
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