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用伪节点进行RNA折叠的动态编程方案的自动设计

Bertrand Marchand^1,2, Sebastian Will¹, Sarah J Berkemer^1,3

¹LIX (UMR 7161), Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France.

Algorithms for molecular biology : AMB

|December 2, 2023

概括

我们开发了一种自动化的方法来设计动态编程 (DP) 算法用于RNA伪结的预测. 这种方法概括了现有的方法,并实现了高效,可预测的RNA折叠分析.

科学领域:

计算生物学计算生物学
生物信息学是一种生物信息学.
RNA结构分析RNA结构分析

背景情况:

预测RNA二级结构通常使用动态编程 (DP) 来解决.
预测使用伪结的RNA结构在计算上具有挑战性 (NP-hard),并且通常需要针对特定结构的专门,手工制作的DP算法.
现有的伪结预测方法仅限于RNA构造的受限类.

研究的目的:

概括和自动化DP算法的设计用于RNA伪结的预测.
开发一个用于自动生成DP方案的框架,使RNA折叠的算法复杂性最小化.
为了处理更广泛的RNA形状,超出了无语境语法.

主要方法:

使用脂肪图形式化DP算法设计问题,用于使用脂肪图的构造类.
开发基于代表性结构的树分解算法来生成DP方案.
证明基于脂肪图的树宽度的伪结预测的固定参数可操作性.

主要成果:

拟议的方法自动生成DP算法,其复杂性与用于常见伪结类的手工算法相比较.
该框架的时间复杂性为O(n^3) (或O(n^2) 对于更简单的模型),其中n是RNA长度.
生成的算法支持一般的能量模型,分区函数计算和部分折叠.

结论:

DP算法的自动设计为RNA伪结预测提供了一种强大而灵活的方法.
这种方法将复杂RNA结构的高效算法的创建概括和简化.
该框架有可能推进代数动态编程,超越无上下文结构.

关键词:

这些是伪结.在RNA折叠过程中.树的分解树的分解树的宽度树的宽度

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