Pfold: RNA secondary structure prediction using stochastic context-free grammars
Pfold: RNA secondary structure prediction using stochastic context-free grammars
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DOI：
10.1093/nar/gkg614
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发表时间：
2003-07-01
影响因子：
14.9
通讯作者：
Hein, J
中科院分区：
文献类型：
--
作者：
Knudsen, B;Hein, J
RNA二级结构在许多生物过程中起着重要的作用，有效的结构预测可以为实验研究提供重要的指导。许多用于RNA二级结构预测的可用程序一次仅使用单个序列。这在某些应用中可能是足够的，但通常可以获得具有保守二级结构的相关RNA序列。这些应包括在结构分析中，以提供更好的结果。这项工作提出了一种预测RNA二级结构的实用方法，当可以获得相关序列时特别有用。该方法改进了以往基于显式进化模型和概率模型的算法。预测可以在http://www.daimi.au.dk/similar tocompbio/pfold的网络服务器上完成。
RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs for RNA secondary structure prediction only use a single sequence at a time. This may be sufficient in some applications, but often it is possible to obtain related RNA sequences with conserved secondary structure. These should be included in structural analyses to give improved results. This work presents a practical way of predicting RNA secondary structure that is especially useful when related sequences can be obtained. The method improves a previous algorithm based on an explicit evolutionary model and a probabilistic model of structures. Predictions can be done on a web server at http://www.daimi.au.dk/similar tocompbio/pfold.