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Methods. 2019 Jun 1;162-163:60-67. doi: 10.1016/j.ymeth.2019.04.003. Epub 2019 Apr 2.

How to benchmark RNA secondary structure prediction accuracy.

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Center for RNA Biology, Department of Biochemistry & Biophysics, and Department of Biostatistics & Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, United States. Electronic address:


RNA secondary structure prediction is widely used. As new methods are developed, these are often benchmarked for accuracy against existing methods. This review discusses good practices for performing these benchmarks, including the choice of benchmarking structures, metrics to quantify accuracy, the importance of allowing flexibility for pairs in the accepted structure, and the importance of statistical testing for significance.


Comparative sequence analysis; RNA folding

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