ChainKnot: a comparative H-type pseudoknot prediction tool using multiple ab initio folding tools

Authors:
Jikai Lei;Prapaporn Techa-angkoon;Yanni Sun;Rujira Achawanantakun
Affiliations:
Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A.;Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A.;Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A.;Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A.
Venue:
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Year:
2013

Citing 12
Cited 0

Algorithms on strings, trees, and sequences: computer science and computational biology

Algorithms on strings, trees, and sequences: computer science and computational biology
Prediction of Consensus RNA Secondary Structures Including Pseudoknots

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots

Bioinformatics
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons

Bioinformatics
A heuristic approach for detecting RNA H-type pseudoknots

Bioinformatics
Probalign: multiple sequence alignment using partition function posterior probabilities

Bioinformatics
An empirical evaluation of deep architectures on problems with many factors of variation

Proceedings of the 24th international conference on Machine learning
LIBSVM: A library for support vector machines

ACM Transactions on Intelligent Systems and Technology (TIST)
IPknot

Bioinformatics
TurboKnot

Bioinformatics
HFold: RNA pseudoknotted secondary structure prediction using hierarchical folding

WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-Dimensional Chain Algorithm

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

Quantified Score

Hi-index	0.00

Visualization

Abstract

Pseudoknot is an important structural motif in many types of ncRNAs. However, the accuracy of pseudoknot derivation is still not satisfactory even for simple pseudoknotted structures and short sequences. In this work, we design and implement an effective pipeline, ChainKnot, for deriving secondary structures containing recursive H-type pseudoknots from two or multiple ncRNA sequences. ChainKnot solves the consensus structure derivation problem using an extended maximum-weighted chain algorithm. In addition, ChainKnot tests a new strategy that extracts structural elements from the optimal and sub-optimal predictions of multiple ab initio pseudoknot prediction tools. The experimental results on over five hundreds of pseudoknot-containing ncRNAs demonstrate that extracting stems from the output of ab initio tools significantly increases the performance of the prediction pipeline compared to using base-pairing probability matrices. Our approach achieves better sensitivity, PPV, and F-score than the state-of-the-art pseudoknot prediction tools on recursive H-type pseudoknots. The source code of ChainKnot is available at http://sourceforge.net/projects/chainknot