An iterative loop matching approach to the prediction of RNA secondary structures with pseudoknots

J. Ruan, G. D. Stormo, W. Zhang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

In this paper we present a heuristic algorithm, iterative loop matching, for predicting RNA pseudoknots. The method can utilize either thermodynamic or comparative information or both, thus is able to predict for both aligned and individual sequences. Using 8-12 homologous sequences, the algorithm correctly identifies more than 90% of base-pairs for short sequences and 80% overall. It correctly predicts nearly all pseudoknots, while having very few false predictions. Comparisons show that our algorithm is more sensitive and more specific than existing methods. In addition, our algorithm is very efficient and can be applied to sequences up to several thousands of bases long.

Original languageEnglish (US)
Title of host publicationProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages519-520
Number of pages2
ISBN (Electronic)0769520006, 9780769520001
DOIs
StatePublished - 2003
Externally publishedYes
Event2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States
Duration: Aug 11 2003Aug 14 2003

Publication series

NameProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Conference

Conference2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
CountryUnited States
CityStanford
Period8/11/038/14/03

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Computer Science Applications

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  • Cite this

    Ruan, J., Stormo, G. D., & Zhang, W. (2003). An iterative loop matching approach to the prediction of RNA secondary structures with pseudoknots. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003 (pp. 519-520). [1227394] (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CSB.2003.1227394