TY - GEN

T1 - Approximate periodicity

AU - Amir, Amihood

AU - Eisenberg, Estrella

AU - Levy, Avivit

PY - 2010

Y1 - 2010

N2 - We consider the question of finding an approximate period in a given string S of length n. Let S′ be a periodic string closest to S under some distance metric. We consider this distance the error of the periodic string, and seek the smallest period that generates a string with this distance to S. In this paper we consider the Hamming and swap distance metrics. In particular, if S is the given string, and S′ is the closest periodic string to S under the Hamming distance, and if that distance is k, we develop an O(nkloglogn) algorithm that constructs the smallest period that defines such a periodic string S′. We call that string the approximate period of S under the Hamming distance. We further develop an O(n 2) algorithm that constructs the approximate period under the swap distance. Finally, we show an O(nlogn) algorithm for finite alphabets, and O(nlog3 n) algorithm for infinite alphabets, that approximates the number of mismatches in the approximate period of the string.

AB - We consider the question of finding an approximate period in a given string S of length n. Let S′ be a periodic string closest to S under some distance metric. We consider this distance the error of the periodic string, and seek the smallest period that generates a string with this distance to S. In this paper we consider the Hamming and swap distance metrics. In particular, if S is the given string, and S′ is the closest periodic string to S under the Hamming distance, and if that distance is k, we develop an O(nkloglogn) algorithm that constructs the smallest period that defines such a periodic string S′. We call that string the approximate period of S under the Hamming distance. We further develop an O(n 2) algorithm that constructs the approximate period under the swap distance. Finally, we show an O(nlogn) algorithm for finite alphabets, and O(nlog3 n) algorithm for infinite alphabets, that approximates the number of mismatches in the approximate period of the string.

UR - http://www.scopus.com/inward/record.url?scp=78650873446&partnerID=8YFLogxK

U2 - 10.1007/978-3-642-17517-6_5

DO - 10.1007/978-3-642-17517-6_5

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AN - SCOPUS:78650873446

SN - 3642175163

SN - 9783642175169

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 25

EP - 36

BT - Algorithms and Computation - 21st International Symposium, ISAAC 2010, Proceedings

T2 - 21st Annual International Symposium on Algorithms and Computations, ISAAC 2010

Y2 - 15 December 2010 through 17 December 2010

ER -