基于亏格过滤的RNA伪纽结结构的均匀生成
Uniform generation of RNA pseudoknot structures with genus filtration
摘要：
本文提出了一个固定拓扑亏格的RNA结构抽样框架。我们介绍了一种新的，线性时间，均匀采样算法的RNA结构的固定拓扑亏格$g$，任意$g>0$。此外，我们开发了一个线性时间采样算法的RNA结构的固定拓扑属$g$，加权的简化，基于循环的能量泛函。对于该过程，能量泛函的配分函数必须计算一次，其具有$O(n^2)$时间复杂度。
英文摘要：
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 this process the partition function of the energy functional has to be computed once, which has $O(n^2)$ time complexity.
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