Pattern matching for arc-annotated sequences

Authors:
Jens Gramm;Jiong Guo;Rolf Niedermeier
Affiliations:
Universität Tübingen, Tübingen, Germany;Friedrich-Schiller-Universität Jena, Jena, Germany;Friedrich-Schiller-Universität Jena, Jena, Germany
Venue:
ACM Transactions on Algorithms (TALG)
Year:
2006

Citing 10
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Abstract

We study pattern matching for arc-annotated sequences. An O(nm) time algorithm is given for the problem to determine whether a length m sequence with nested arc annotation is an arc-preserving subsequence (aps) of a length n sequence with nested arc annotation, called APS(NESTED,NESTED). Arc-annotated sequences and, in particular, those with nested arc annotation are motivated by applications in RNA structure comparison. Our algorithm generalizes results for ordered tree inclusion problems and it is useful for recent fixed-parameter algorithms for LAPCS(NESTED,NESTED), which is the problem of computing a longest arc-preserving common subsequence of two sequences with nested arc annotations. In particular, the presented dynamic programming methodology implies a quadratic-time algorithm for an open problem posed by Vialette.