Abstract
We revisit the problem of indexing a string S[1..n] to support searching all substrings in S that match a given pattern P[1..m] with at most k errors. Previous solutions either require an index of size exponential in k or need Ω(m k) time for searching. Motivated by the indexing of DNA sequences, we investigate space efficient indexes that occupy only O(n) space. For k = 1, we give an index to support matching in O(m + occ + logn loglogn) time. The previously best solution achieving this time complexity requires an index of size O(n logn). This new index can be used to improve existing indexes for k ≥2 errors. Among others, it can support matching with k=2 errors in O(m logn loglogn + occ) time.
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Chan, HL., Lam, TW., Sung, WK., Tam, SL., Wong, SS. (2006). Compressed Indexes for Approximate String Matching. In: Azar, Y., Erlebach, T. (eds) Algorithms – ESA 2006. ESA 2006. Lecture Notes in Computer Science, vol 4168. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11841036_21
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DOI: https://doi.org/10.1007/11841036_21
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-38875-3
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