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Faster algorithms for 1-mappability of a sequence
[article]

2017
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arXiv
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pre-print

In the k-mappability problem, we are given a string x of length n and integers m and k, and we are asked to count, for each length-m factor y of x, the number of other factors of length m of x that are at Hamming distance at most k from y. We focus here on the version of the problem where k = 1. The fastest known algorithm for k = 1 requires time O(mn log n/ log log n) and space O(n). We present two algorithms that require worst-case time O(mn) and O(n log^2 n), respectively, and space O(n),

arXiv:1705.04022v1
fatcat:xh4iqa7ufvbgzfgofmizebfiie