145 research outputs found

    On Indeterminate Strings Matching

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    Order-Preserving Squares in Strings

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    Fast Entropy-Bounded String Dictionary Look-Up with Mismatches

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    We revisit the fundamental problem of dictionary look-up with mismatches. Given a set (dictionary) of d strings of length m and an integer k, we must preprocess it into a data structure to answer the following queries: Given a query string Q of length m, find all strings in the dictionary that are at Hamming distance at most k from Q. Chan and Lewenstein (CPM 2015) showed a data structure for k = 1 with optimal query time O(m/w + occ), where w is the size of a machine word and occ is the size of the output. The data structure occupies O(w d log^{1+epsilon} d) extra bits of space (beyond the entropy-bounded space required to store the dictionary strings). In this work we give a solution with similar bounds for a much wider range of values k. Namely, we give a data structure that has O(m/w + log^k d + occ) query time and uses O(w d log^k d) extra bits of space

    Two algorithms for LCS Consecutive Suffix Alignment

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    AbstractThe problem of aligning two sequences A and B to determine their similarity is one of the fundamental problems in pattern matching. A challenging, basic variation of the sequence similarity problem is the incremental string comparison problem, denoted Consecutive Suffix Alignment, which is, given two strings A and B, to compute the alignment solution of each suffix of A versus B.Here, we present two solutions to the Consecutive Suffix Alignment Problem under the LCS (Longest Common Subsequence) metric, where the LCS metric measures the subsequence of maximal length common to A and B. The first solution is an O(nL) time and space algorithm for constant alphabets, where the size of the compared strings is O(n) and L⩽n denotes the size of the LCS of A and B.The second solution is an O(nL+nlog|Σ|) time and O(n) space algorithm for general alphabets, where Σ denotes the alphabet of the compared strings
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