Efficient detection of quasiperiodicities in strings
Theoretical Computer Science
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
Efficient randomized pattern-matching algorithms
IBM Journal of Research and Development - Mathematics and computing
Algorithms on Strings
An algorithmic framework for motif discovery problems in weighted sequences
CIAC'10 Proceedings of the 7th international conference on Algorithms and Complexity
On left and right seeds of a string
Journal of Discrete Algorithms
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Finding repeating patterns is a useful operation that have application in fields such as computing, music and molecular biology. In the latter, a requirement to detect repeating patterns in nucleic or protein sequences are very common in many applications such as the assembling of a genome from fragments. Finding covers and seeds of biological sequences have been equally important and useful operations in these fields. Algorithms that efficiently find covers and seeds of strings have been described in many papers. We focus in this paper on special cases of finding the shortest seeds in a weighted sequence with presence probability not less than a given threshold. Finding repeating patterns is a useful operation that have application in fields such as computing, music and molecular biology. In the latter, a requirement to detect repeating patterns in nucleic or protein sequences are very common in many applications such as the assembling of a genome from fragments. Finding covers and seeds of biological sequences have been equally important and useful operations in these fields. Algorithms that efficiently find covers and seeds of strings have been described in many papers. We focus in this paper on special cases of finding the shortest seeds in a weighted sequence with presence probability not less than a given threshold. A weighted sequence is a string in which a set of characters may appear at each position with respective probabilities of occurrence. In this paper we propose an O(nlogn) algorithm for finding the shortest seeds of a weighted sequence, where n is the cardinality of the input sequence, based on the algorithms for computing all the repeats of every length by using an iterative partitioning technique.