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

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

doi:10.1109/CSB.2003.1227394

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 proceeding › Conference contribution › peer-review

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 language	English
Title of host publication	Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	519-520
Number of pages	2
ISBN (Electronic)	0769520006, 9780769520001
DOIs	https://doi.org/10.1109/CSB.2003.1227394
State	Published - 2003
Event	2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States Duration: Aug 11 2003 → Aug 14 2003

Publication series

Name	Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Conference

Conference	2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
Country/Territory	United States
City	Stanford
Period	08/11/03 → 08/14/03

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10.1109/CSB.2003.1227394

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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). Article 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

@inproceedings{e367ac781c4f4dfe8162bce0e48b758a,

title = "An iterative loop matching approach to the prediction of RNA secondary structures with pseudoknots",

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.",

author = "J. Ruan and Stormo, {G. D.} and W. Zhang",

note = "Publisher Copyright: {\textcopyright} 2003 IEEE.; 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 ; Conference date: 11-08-2003 Through 14-08-2003",

year = "2003",

doi = "10.1109/CSB.2003.1227394",

language = "English",

series = "Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "519--520",

booktitle = "Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003",

}

Ruan, J, Stormo, GD & 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., 1227394, Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003, Institute of Electrical and Electronics Engineers Inc., pp. 519-520, 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003, Stanford, United States, 08/11/03. https://doi.org/10.1109/CSB.2003.1227394

An iterative loop matching approach to the prediction of RNA secondary structures with pseudoknots. / Ruan, J.; Stormo, G. D.; Zhang, W.
Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 519-520 1227394 (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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N2 - 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.

AB - 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.

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T3 - Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

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BT - Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003

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

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

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