Combinatorics of saturated secondary structures of RNA
Combinatorics of saturated secondary structures of RNA
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DOI：
10.1089/cmb.2006.13.1640
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发表时间：
2006-11-01
影响因子：
1.7
通讯作者：
Clote, P.
中科院分区：
文献类型：
--
作者：
Clote, P.
根据Zuker（1986），给定RNA序列的饱和二级结构是这样的二级结构，即在不违反二级结构定义的情况下，不能添加碱基对。例如，在一个实施例中，而不引入假结。在Nussinov-Jacobson能量模型（Nussinov and Jacobson，1980）中，二级结构的能量是碱基对数量的-1倍，饱和二级结构是能量景观中的局部最小值，因此在折叠过程中形成动力学陷阱。在这里，我们提出的递归关系和封闭形式的渐近极限的饱和二级结构的数量相关的组合问题。此外，用于计算具有k个碱基对的饱和二级结构的数量的Python源代码可以在bioinformatics.bc.edu/clotelab/的web服务器链接中找到。
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 secondary structures are local minima in the energy landscape, hence form kinetic traps during the folding process. Here we present recurrence relations and closed form asymptotic limits for combinatorial problems related to the number of saturated secondary structures. In addition, Python source code to compute the number of saturated secondary structures having k base pairs can be found at the web servers link of bioinformatics.bc.edu/clotelab/.