Querying highly similar sequences
by Carl Barton; Mathieu Giraud; Costas S. Iliopoulos; Thierry Lecroq; Laurent Mouchard; Solon P. Pissis
International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 6, No. 1/2, 2013

Abstract: In this paper, we present a solution to the extreme similarity sequencing problem. The extreme similarity sequencing problem consists of finding occurrences of a pattern p in a set S₀, S₁, …, S_k, of sequences of equal length, where S_i, for all 1≤i≤k, differs from S₀ by a constant number of errors - around 10 in practice. We present an asymptotically fast O(n + occ logocc) time algorithm, as well as a practical O(nk/w) time algorithm for solving this problem, where n is the length of a sequence, occ is the number of candidate occurrences reported by our technique, w is the size of the machine word, and the total number of errors is bounded by k - the number of sequences.

Online publication date: Thu, 18-Sep-2014

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