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Subwords in Reverse-Complement Order
Péter L. Erdős1, Péter Ligeti2, Péter Sziklai2, and David C. Torney3
1A. Rényi Institute of Mathematics, Hungarian Academy of Sciences, Budapest, P.O. Box 127, H-1364, Hungary
elp@renyi.hu
2Department of Computer Science, Eötvös University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
{turul, sziklai}@cs.elte.hu
3Theoretical Biology and Biophysics, Mailstop K710, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
dtorney@earthlink.net
Annals of Combinatorics 10 (4) p.415-430 December, 2006
AMS Subject Classification: 05D05, 68R15
Abstract:
We examine finite words over an alphabet of pairs of letters, where each word w1w2wt is identified with its reverse complement (where ). We seek the smallest k such that every word of length n, composed from Γ, is uiquely determined by the set of its subwords of length up to k. Our almost sharp result is an analogue of a classical result for “normal” words. This problem has its roots in bioinformatics.
Keywords: combinatorics of words, Levenshtein distance, DNA codes, reconstruction of words

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