منابع مشابه
Canonical RNA Pseudoknot Structures
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...
متن کاملLoops in Canonical RNA Pseudoknot Structures
In this article, we compute the limit distributions of the numbers of hairpin-loops, interior-loops and bulges in k-noncrossing RNA structures. The latter are coarse-grained RNA structures allowing for cross-serial interactions, subject to the constraint that there are at most k - 1 mutually crossing arcs in the diagram representation of the molecule. We prove central limit theorems by means of...
متن کاملShapes of RNA Pseudoknot Structures
In this article, we study abstract shapes of k-noncrossing, σ-canonical RNA pseudoknot structures. We consider lv1k- and lv5k-shapes, which represent a generalization of the abstract π'- and π-shapes of RNA secondary structures introduced by Giegerich et al. Using a novel approach, we compute the generating functions of lv1k- and lv5k-shapes as well as the generating functions of all lv1k- and ...
متن کاملFolding 3-Noncrossing RNA Pseudoknot Structures
In this article, we present the novel ab initio folding algorithm cross, which generates minimum free energy (mfe), 3-noncrossing, canonical RNA structures. Here an RNA structure is 3-noncrossing if it does not contain three or more mutually crossing arcs and canonical, if each of its stacks has size greater or equal than two. Our notion of mfe-structure is based on a specific concept of pseudo...
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In this paper we present a sampling framework for RNA structures of fixed topological genus. We introduce a novel, linear time, uniform sampling algorithm for RNA structures of fixed topological genus g, for arbitrary g > 0. Furthermore we develop a linear time sampling algorithm for RNA structures of fixed topological genus g that are weighted by a simplified, loop-based energy functional. For...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2008
ISSN: 1066-5277,1557-8666
DOI: 10.1089/cmb.2008.0121