INFO-RNA - a fast approach to inverse RNA folding
INFO-RNA - a fast approach to inverse RNA folding
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DOI：
10.1093/bioinformatics/btl194
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发表时间：
2006-08-01
期刊：
影响因子：
5.8
通讯作者：
Backofen, Rolf
中科院分区：
文献类型：
--
作者：
Busch, Anke;Backofen, Rolf
动机：RNA分子的结构通常对其功能至关重要。因此，二级结构预测受到了广泛的关注。在这里，我们考虑的逆RNA折叠问题，这意味着设计RNA序列折叠成一个给定的structure.Results：我们介绍了一种新的算法的逆折叠问题（INFO-RNA），由两部分组成;一个动态规划方法，良好的初始序列和以下改进的随机局部搜索，使用一个有效的邻居选择方法。在初始化过程中，我们设计了一个序列，在所有序列中采用给定的结构，具有最低的能量。对于在搜索过程中的邻居的选择，我们使用一种前瞻性的一个选择步骤应用一个额外的基于能量的标准。然后，利用最小化目标结构与所考虑的近邻的mfe结构之间的结构距离的实际优化准则对预排序近邻进行测试，并在人工测试集和生物测试集上与RNAinverse和RNA-SSD算法进行了比较。使用INFO-RNA，我们的表现优于RNAinverse，在大多数情况下，我们获得了比RNA-SSD更好的结果，RNA-SSD可能是市场上最好的反向RNA折叠工具。
Motivation: The structure of RNA molecules is often crucial for their function. Therefore, secondary structure prediction has gained much interest. Here, we consider the inverse RNA folding problem, which means designing RNA sequences that fold into a given structure.Results: We introduce a new algorithm for the inverse folding problem (INFO-RNA) that consists of two parts; a dynamic programming method for good initial sequences and a following improved stochastic local search that uses an effective neighbor selection method. During the initialization, we design a sequence that among all sequences adopts the given structure with the lowest possible energy. For the selection of neighbors during the search, we use a kind of look-ahead of one selection step applying an additional energy-based criterion. Afterwards, the pre-ordered neighbors are tested using the actual optimization criterion of minimizing the structure distance between the target structure and the mfe structure of the considered neighbor.We compared our algorithm to RNAinverse and RNA-SSD for artificial and biological test sets. Using INFO-RNA, we performed better than RNAinverse and in most cases, we gained better results than RNA-SSD, the probably best inverse RNA folding tool on the market.