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 [Erdős et al., Ann. of Comb. 2006].
This research was carried out in part while F.C. and Zs.L. were visiting with the Alfréd Rényi Institute in Budapest, with support from the Hungarian Bioinformatics MTKD-CT-2006-042794, Marie Curie Host Fellowships for Transfer of Knowledge.
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Cicalese, F., Erdős, P.L., Lipták, Z. (2011). Efficient Reconstruction of RC-Equivalent Strings. In: Iliopoulos, C.S., Smyth, W.F. (eds) Combinatorial Algorithms. IWOCA 2010. Lecture Notes in Computer Science, vol 6460. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19222-7_35
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DOI: https://doi.org/10.1007/978-3-642-19222-7_35
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