In the reverse complement equivalence model, it is not possible to distinguish a string from its reverse complement. We show that one can still reconstruct a string of length n, up to reverse complement, using a linear number of subsequence queries of bounded length. We first give the proof for strings over a binary alphabet, and then extend it to arbitrary finite alphabets. A simple information theoretic lower bound proves the number of queries to be asymptotically tight. Furthermore, our result is optimal w.r.t. the bound on the query length given in [Erd ̋os et al., Ann. of Comb. 2006].

A Linear Algorithm for String Reconstruction in the Reverse Complement Equivalence Model

Liptak, Zsuzsanna
2012

Abstract

In the reverse complement equivalence model, it is not possible to distinguish a string from its reverse complement. We show that one can still reconstruct a string of length n, up to reverse complement, using a linear number of subsequence queries of bounded length. We first give the proof for strings over a binary alphabet, and then extend it to arbitrary finite alphabets. A simple information theoretic lower bound proves the number of queries to be asymptotically tight. Furthermore, our result is optimal w.r.t. the bound on the query length given in [Erd ̋os et al., Ann. of Comb. 2006].
string reconstruction, reverse complement, string algorithms, subsequences, subwords, combinatorics on words
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11562/391082
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