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Efficient algorithm for testing structure freeness of finite set of biomolecular sequences. (English) Zbl 1234.68113
Carbone, Alessandra (ed.) et al., DNA computing. 11th international workshops on DNA computing, DNA11, London, ON, Canada, June 6–9, 2005. Revised selected papers. Berlin: Springer (ISBN 3-540-34161-7/pbk). Lecture Notes in Computer Science 3892, 171-180 (2006).
Summary: In this paper we will focus on the structure freeness test problem of finite sets of sequences. The result is an extension of Andronescu’s algorithm which can be applied to the sequence design of various DNA computing experiments. We will first give a general algorithm for this problem which runs in \(O(n^{5})\) time. Then, we will give an evaluation method for sequence design system, which requires \(O(n^{5})\) time for precomputation, and \(O(n^{4})\) time and \(O(n^{5})\) space for each evaluation of sequence sets. The authors believe that this result will give an important progress of efficient sequence design systems.
For the entire collection see [Zbl 1096.68002].
MSC:
68Q10 Modes of computation (nondeterministic, parallel, interactive, probabilistic, etc.)
68Q05 Models of computation (Turing machines, etc.) (MSC2010)
68Q25 Analysis of algorithms and problem complexity
92D20 Protein sequences, DNA sequences
Software:
ViennaRNA
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References:
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