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

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article number6374371
Pages (from-to)691-700
Number of pages10
JournalTsinghua Science and Technology
Volume17
Issue number6
DOIs
StatePublished - Dec 1 2012

All Science Journal Classification (ASJC) codes

  • General

Keywords

  • RNA structure
  • pseudoknots
  • tool ensemble

Fingerprint Dive into the research topics of 'Using folding ensemble and stem probability maximization methods to predict RNA H-type pseudoknots'. Together they form a unique fingerprint.

Cite this