Recent advances in RNA secondary structure prediction with pseudoknots
Recent advances in RNA secondary structure prediction with pseudoknots
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DOI：
10.2174/157489306777011996
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发表时间：
2006-05-01
影响因子：
4
通讯作者：
Akutsu, Tatsuya
中科院分区：
文献类型：
--
作者：
Akutsu, Tatsuya
最近人们认识到RNA的伪结点具有重要的作用，并且相当数量的RNA含有伪结点。因此，最近对RNA二级结构预测的研究主要集中在假结上。基于动态规划的几种算法已经被开发出来。虽然解决方案的最优性得到了保证，但这些算法存在时间复杂度高的问题。因此，启发式算法也被开发出来，其中一些算法被认为可以在合理的CPU时间内产生接近最优解。最近，又提出了一种基于比较建模的方法。在上述算法的基础上，开发了一些实用程序和基于Web的服务器程序。本文旨在介绍利用伪结点预测RNA二级结构的重要算法的基本思想。本文还试图揭示重要算法之间的关系。
It has recently been recognized that pseudoknots of RNAs have important roles and not a small number of RNAs contain pseudoknots. Therefore, recent studies on RNA secondary structure prediction focus on pseudoknots. Several algorithms have been developed based on dynamic programming. Though optimality of a solution is guaranteed, these algorithms suffer from high time complexities. Thus, heuristic algorithms have also been developed, some of which are supposed to produce near optimal solutions in reasonable CPU time. Recently, another approach based on comparative modeling has been proposed. Several practical programs and web-based server programs are also developed based on the above-mentioned algorithms. The purpose of this review paper is to introduce the basic ideas in important algorithms for RNA secondary structure prediction with pseudoknots. This paper also tries to reveal relations among important algorithms.