Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA.
RNA. 2010 Oct;16(10):1870-80. doi: 10.1261/rna.2125310. Epub 2010 Aug 10.
It is a significant challenge to predict RNA secondary structures including pseudoknots. Here, a new algorithm capable of predicting pseudoknots of any topology, ProbKnot, is reported. ProbKnot assembles maximum expected accuracy structures from computed base-pairing probabilities in O(N(2)) time, where N is the length of the sequence. The performance of ProbKnot was measured by comparing predicted structures with known structures for a large database of RNA sequences with fewer than 700 nucleotides. The percentage of known pairs correctly predicted was 69.3%. Additionally, the percentage of predicted pairs in the known structure was 61.3%. This performance is the highest of four tested algorithms that are capable of pseudoknot prediction. The program is available for download at: http://rna.urmc.rochester.edu/RNAstructure.html.
预测包括假结在内的 RNA 二级结构是一项重大挑战。这里报告了一种新的算法 ProbKnot，它能够预测任何拓扑结构的假结。ProbKnot 通过在 O(N(2))时间内从计算出的碱基配对概率中组装出最大期望精度的结构，其中 N 是序列的长度。通过将预测结构与具有少于 700 个核苷酸的大型 RNA 序列数据库的已知结构进行比较，来测量 ProbKnot 的性能。正确预测的已知碱基对的百分比为 69.3%。此外，已知结构中预测碱基对的百分比为 61.3%。这一性能是四种能够进行假结预测的测试算法中的最高水平。该程序可在以下网址下载：http://rna.urmc.rochester.edu/RNAstructure.html。
