Abstract
In this work, we consider a special type of uncertain sequence called weighted string. In a weighted string every position contains a subset of the alphabet and every letter of the alphabet is associated with a probability of occurrence such that the sum of probabilities at each position equals 1. Usually a cumulative weight threshold 
is specified, and one considers only strings that match the weighted string with probability at least 
. We provide an \(\mathcal {O}(nz)\)-time and \(\mathcal {O}(nz)\)-space off-line algorithm, where n is the length of the weighted string and 
is the given threshold, to compute a smallest maximal palindromic factorization of a weighted string. This factorization has applications in hairpin structure prediction in a set of closely-related DNA or RNA sequences. Along the way, we provide an \(\mathcal {O}(nz)\)-time and \(\mathcal {O}(nz)\)-space off-line algorithm to compute maximal palindromes in weighted strings.
M. Alzamel and C.S. Iliopoulos—Partially supported by the Onassis Foundation.
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Alzamel, M., Gao, J., Iliopoulos, C.S., Liu, C., Pissis, S.P. (2017). Efficient Computation of Palindromes in Sequences with Uncertainties. In: Boracchi, G., Iliadis, L., Jayne, C., Likas, A. (eds) Engineering Applications of Neural Networks. EANN 2017. Communications in Computer and Information Science, vol 744. Springer, Cham. https://doi.org/10.1007/978-3-319-65172-9_52
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