memerna:稀疏 RNA 折叠(包括同轴堆积)。

IF 4.7 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Biology Pub Date : 2024-10-18 DOI:10.1016/j.jmb.2024.168819
Eliot Courtney, Amitava Datta, David H Mathews, Max Ward
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引用次数: 0

摘要

确定 RNA 二级结构是计算生物学的核心问题。美国纽约州罗切斯特市罗切斯特大学医学中心生物化学与生物物理学系 我们描述了一种带有同轴堆叠的 Zuker-Stiegler 算法的改进公式,同轴堆叠是一种稳定的相互作用,在这种相互作用中,多环中螺旋的末端被堆叠起来。特别是,最优同轴堆叠的计算是动态编程状态的一部分,而不是在内环中进行。我们引入了一个新的稀疏性概念,称之为可替换性。与之前的稀疏折叠方法使用的三角形不等式相比,可替换性是一个更通用的条件,适用于更多地方。我们还引入了非单调候选列表作为额外的稀疏化工具。现有的用于稀疏折叠的三角形不等式可以看作是可替换性和单调性的结合应用。修改后的递归和可替换性使稀疏化也能应用于同轴堆叠,从而提高了算法的速度。我们在名为 memerna 的软件中实现了这一算法,结果表明,在支持同轴堆积的完整 Turner 2004 模型下,该软件是 RNA 折叠的最快精确(非启发式)实现工具。我们还引入了一种新的二级结构符号,其中包括同轴堆积、末端错配和悬垂(CTDs)信息。memerna软件包0.1版本可在https://github.com/Edgeworth/memerna/tree/release/0.1。
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memerna: Sparse RNA Folding Including Coaxial Stacking.

Determining RNA secondary structure is a core problem in computational biology. Fast algorithms for predicting secondary structure are fundamental to this task.Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY, USA We describe a modified formulation of the Zuker-Stiegler algorithm with coaxial stacking, a stabilising interaction in which the ends of helices in multi-loops are stacked. In particular, optimal coaxial stacking is computed as part of the dynamic programming state, rather than in an inner loop. We introduce a new notion of sparsity, which we call replaceability. Replaceability is a more general condition and applicable in more places than the triangle inequality that is used by previous sparse folding methods. We also introduce non-monotonic candidate lists as an additional sparsification tool. Existing usages of the triangle inequality for sparsification can be thought of as an application of both replaceability and monotonicity together. The modified recurrences along with replaceability allows sparsification to be applied to coaxial stacking as well, which increases the speed of the algorithm. We implemented this algorithm in software we call memerna, which we show to have the fastest exact (non-heuristic) implementation of RNA folding under the complete Turner 2004 model with coaxial stacking, out of several popular RNA folding tools supporting coaxial stacking. We also introduce a new notation for secondary structure which includes coaxial stacking, terminal mismatches, and dangles (CTDs) information. The memerna package 0.1 release is available at https://github.com/Edgeworth/memerna/tree/release/0.1.

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来源期刊
Journal of Molecular Biology
Journal of Molecular Biology 生物-生化与分子生物学
CiteScore
11.30
自引率
1.80%
发文量
412
审稿时长
28 days
期刊介绍: Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology; Cell cycle, cell growth, cell differentiation; Cell death, autophagy; Cell signaling and regulation; Chemical biology; Computational biology, in combination with experimental studies; DNA replication, repair, and recombination; Development, regenerative biology, mechanistic and functional studies of stem cells; Epigenetics, chromatin structure and function; Gene expression; Membrane processes, cell surface proteins and cell-cell interactions; Methodological advances, both experimental and theoretical, including databases; Microbiology, virology, and interactions with the host or environment; Microbiota mechanistic and functional studies; Nuclear organization; Post-translational modifications, proteomics; Processing and function of biologically important macromolecules and complexes; Molecular basis of disease; RNA processing, structure and functions of non-coding RNAs, transcription; Sorting, spatiotemporal organization, trafficking; Structural biology; Synthetic biology; Translation, protein folding, chaperones, protein degradation and quality control.
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