Efficient reconstruction of RC-equivalent strings

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 [Erdos et al., Ann. of Comb. 2006]. © 2011 Springer-Verlag.