Inverse folding of RNA pseudoknot structures.
Inverse folding of RNA pseudoknot structures.
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RNA假结结构的反向折叠
DOI：
10.1186/1748-7188-5-27
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发表时间：
2010-06-23
期刊：
影响因子：
--
通讯作者：
Reidys CM
中科院分区：
文献类型：
--
作者：
Gao JZ;Li LY;Reidys CM
RNA具有多种结构构型。在这里，我们认为一个结构等同于非交叉沃森-克里克和G-U-碱基配对（二级结构）和额外的交叉序列碱基对。这些相互作用被称为假结，并且在整个RNA功能谱中观察到。在研究天然RNA结构、寻找新的核酶和设计人工RNA的背景下，发现折叠成特定结构的RNA序列并分析其诱导的中性网络是令人感兴趣的。由于已建立的反向折叠算法RNAinverse、RNA-SSD和INFO-RNA仅限于RNA二级结构，本文提出了一种能处理3-非交叉、规范伪结结构的反向折叠算法Inv。在本文中，我们提出了反折叠算法Inv。我们给出了一个详细的分析，包括伪代码。我们表明，Inv允许设计，特别是3-noncrossing nonplanar RNA pseudoknot 3-noncrossing RNA structures-a class，这是很难通过动态编程例程构建。Inv可在http://www.combinatorics.cn/cbpc/inv.html上免费获得。算法Inv将逆折叠能力扩展到RNA伪结结构。与RNAinverse相比，它使用了新的想法，例如通过考虑竞争结构的集合。因此，Inv不仅能够找到新的序列，甚至是RNA二级结构，它也能在潜在表现出交叉序列相互作用的竞争结构的背景下找到新的序列。
RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure) and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms, RNAinverse, RNA-SSD as well as INFO-RNA are limited to RNA secondary structures, we present in this paper the inverse folding algorithm Inv which can deal with 3-noncrossing, canonical pseudoknot structures. In this paper we present the inverse folding algorithm Inv. We give a detailed analysis of Inv, including pseudocodes. We show that Inv allows to design in particular 3-noncrossing nonplanar RNA pseudoknot 3-noncrossing RNA structures-a class which is difficult to construct via dynamic programming routines. Inv is freely available at http://www.combinatorics.cn/cbpc/inv.html. The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures. In comparison with RNAinverse it uses new ideas, for instance by considering sets of competing structures. As a result, Inv is not only able to find novel sequences even for RNA secondary structures, it does so in the context of competing structures that potentially exhibit cross-serial interactions.
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影响因子：
1.8
作者：
HOFACKER, IL;FONTANA, W;SCHUSTER, P
通讯作者：
SCHUSTER, P
影响因子：
5.6
作者：
BORER, PN;DENGLER, B;UHLENBECK, OC
通讯作者：
UHLENBECK, OC
影响因子：
5.8
作者：
Busch, Anke;Backofen, Rolf
通讯作者：
Backofen, Rolf
预测单链 RNA 二级结构的快速算法
DOI：
10.1073/pnas.77.11.6309
发表时间：
1980-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
NUSSINOV, R;JACOBSON, AB
通讯作者：
JACOBSON, AB
影响因子：
5
作者：
CHAMORRO, A;MANKO, VS;DENISOVA, TE
通讯作者：
DENISOVA, TE