We present in this paper an ab initio method, named KnotFold, for RNA H-type pseudoknot prediction. Our method employs an ensemble of RNA folding tools and a filtering heuristic to generate a set of pseudoknot-free stems, and then predicts pseudoknots by utilizing a search technique with a pseudo-probability scoring scheme. Experimental results show that KnotFold achieves higher sensitivity than existing methods. The KnotFold package with documentation is freely available at http://bioinformatics.njit.edu/KnotFold.
|Original language||English (US)|
|Number of pages||10|
|Journal||Tsinghua Science and Technology|
|State||Published - Dec 1 2012|
All Science Journal Classification (ASJC) codes
- RNA structure
- tool ensemble