Efficient reconstruction of RC-equivalent strings

Authors:
Ferdinando Cicalese;Péter L. Erdös;Zsuzsanna Lipták
Affiliations:
Dipartimento di Informatica ed Applicazioni, University of Salerno, Italy;Alfréd Rényi Institute of Mathematics, Budapest, Hungary;AG Genominformatik, Technische Fakultät, Bielefeld University, Germany
Venue:
IWOCA'10 Proceedings of the 21st international conference on Combinatorial algorithms
Year:
2010

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Abstract

In the reverse complement (RC) equivalence model, it is not possible to distinguish between a string and its reverse complement. We show that one can still reconstruct a binary string of length n, up to reverse complement, using a linear number of subsequence queries of bounded length. A simple information theoretic lower bound proves the number of queries to be tight. Our result is also optimal w.r.t. the bound on the query length given in [Erdös et al., Ann. of Comb. 2006].