Using folding ensemble and stem probability maximization methods to predict RNA H-type pseudoknots

Authors

Junilda Spirollari, Department of Computer Science
Shawn Xiong Wang, California State University, Fullerton
Jason T.L. Wang, Department of Computer Science

Document Type

Article

Publication Date

12-1-2012

Abstract

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. © 1996-2012 Tsinghua University Press.

Identifier

84876215211 (Scopus)

Publication Title

Tsinghua Science and Technology

External Full Text Location

https://doi.org/10.1109/TST.2012.6374371

ISSN

10070214

First Page

691

Last Page

700

Issue

6

Volume

17

Recommended Citation

Spirollari, Junilda; Wang, Shawn Xiong; and Wang, Jason T.L., "Using folding ensemble and stem probability maximization methods to predict RNA H-type pseudoknots" (2012). Faculty Publications. 17973.
https://digitalcommons.njit.edu/fac_pubs/17973