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Enumerating RNA Motifs: A Coding-Theoretic Approach

机译:枚举RNA主题:编码理论方法

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摘要

We consider the problem of enumerating RNA secondary structures that obey a set of structural constraints arising due to the bio-chemical properties of the sugar-phosphate backbone of the strands. The enumeration problem is cast into a framework involving context-free attribute grammars, where the grammars are used to obtain a closed-form expression for the q-generating functions of the constrained objects via the Delest-Fedou "attribute grammar" method. This approach can be viewed as an extension of the paradigm of constrained coding, which was so far used to operates on constraints represented by regular, rather than context-free languages.
机译:我们考虑枚举RNA二级结构的问题,这些二级结构要遵守由于糖链的糖-磷酸主链的生化特性而引起的一系列结构限制。枚举问题被放到涉及上下文无关属性语法的框架中,其中该语法用于通过Delest-Fedou“属性语法”方法获得约束对象的q生成函数的闭式表达式。可以将这种方法看作是约束编码范例的扩展,到目前为止,它已用于对常规语言(而不是上下文无关语言)表示的约束进行操作。

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