ASYMPTOTICS OF CANONICAL AND SATURATED RNA SECONDARY STRUCTURES
نویسندگان
چکیده
منابع مشابه
Asymptotics of Canonical and Saturated RNA Secondary Structures
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366 . n(-3/2) . 2.618034(n). In this paper, we study combinatorial asymptotics for two special subclasses of RNA secondary structures - canonical and saturated structures. Canonical secondary structures are defined to have no lonely (isolated) base pairs. This class of secondary structu...
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Following Zuker (1986), a saturated secondary structure for a given RNA sequence is a secondary structure such that no base pair can be added without violating the definition of secondary structure, e.g., without introducing a pseudoknot. In the Nussinov-Jacobson energy model (Nussinov and Jacobson, 1980), where the energy of a secondary structure is -1 times the number of base pairs, saturated...
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In the absence of chaperone molecules, RNA folding is believed to depend on the distribution of kinetic traps in the energy landscape of all secondary structures. Kinetic traps in the Nussinov energy model are precisely those secondary structures that are saturated, meaning that no base pair can be added without introducing either a pseudoknot or base triple. In this paper, we compute the asymp...
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Abstract Over the last 30 years the development of RNA secondary structure prediction algorithms have been guided and inspired by corresponding combinatorial studies where the RNA molecules are modeled as certain kind of planar graphs. The other way round, new algorithmic ideas gave rise to interesting combinatorial problems asking for a deeper understanding of the structures processed. One suc...
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In this paper, we study k-noncrossing, sigma-canonical RNA pseudoknot structures with minimum arc-length greater or equal to four. Let T(k, sigma)([4])(n) denote the number of these structures. We derive exact enumeration results by computing the generating function T(k, sigma)([4])(z) = summation operator(n) T(k, sigma)([4])(n)z(n) and derive the asymptotic formulas T(k, 3)([4])(n) approximate...
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ژورنال
عنوان ژورنال: Journal of Bioinformatics and Computational Biology
سال: 2009
ISSN: 0219-7200,1757-6334
DOI: 10.1142/s0219720009004333