An evolving automaton for RNA secondary structure prediction

Carlos A.M. Del Carpio, Mohamed Ismael, Eichiro Ichiishi, Michihisa Koyama, Momoji Kubo, Akira Miyamoto

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

Abstract

Conventional methods for RNA 2D structure prediction search for minimal free energy structures. RNA's, however, RNA's do not always adopt global minimum structures. Rather, their structure is the result of the folding pathway followed by the structure in nature, which adopts sub-optimal folds occurring along the pathway. Our algorithm consists of an automaton that generates RNA structures by searching for optimal folding pathways. The automaton is endowed of operations to travel throughout the hyperspace of conformers embedded in a base pairing matrix. Using genetic programming it evolves optimizing its ability to find optimal pathways and finally 2D structures. Comparing the evolving automaton with conventional methods shows its potential.

Original languageEnglish
Title of host publicationInternational Joint Conference on Neural Networks 2006, IJCNN '06
Pages2226-2233
Number of pages8
Publication statusPublished - Dec 1 2006
EventInternational Joint Conference on Neural Networks 2006, IJCNN '06 - Vancouver, BC, Canada
Duration: Jul 16 2006Jul 21 2006

Publication series

NameIEEE International Conference on Neural Networks - Conference Proceedings
ISSN (Print)1098-7576

Other

OtherInternational Joint Conference on Neural Networks 2006, IJCNN '06
CountryCanada
CityVancouver, BC
Period7/16/067/21/06

Fingerprint

RNA
Genetic programming
Free energy

All Science Journal Classification (ASJC) codes

  • Software

Cite this

Del Carpio, C. A. M., Ismael, M., Ichiishi, E., Koyama, M., Kubo, M., & Miyamoto, A. (2006). An evolving automaton for RNA secondary structure prediction. In International Joint Conference on Neural Networks 2006, IJCNN '06 (pp. 2226-2233). [1716388] (IEEE International Conference on Neural Networks - Conference Proceedings).

An evolving automaton for RNA secondary structure prediction. / Del Carpio, Carlos A.M.; Ismael, Mohamed; Ichiishi, Eichiro; Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira.

International Joint Conference on Neural Networks 2006, IJCNN '06. 2006. p. 2226-2233 1716388 (IEEE International Conference on Neural Networks - Conference Proceedings).

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

Del Carpio, CAM, Ismael, M, Ichiishi, E, Koyama, M, Kubo, M & Miyamoto, A 2006, An evolving automaton for RNA secondary structure prediction. in International Joint Conference on Neural Networks 2006, IJCNN '06., 1716388, IEEE International Conference on Neural Networks - Conference Proceedings, pp. 2226-2233, International Joint Conference on Neural Networks 2006, IJCNN '06, Vancouver, BC, Canada, 7/16/06.
Del Carpio CAM, Ismael M, Ichiishi E, Koyama M, Kubo M, Miyamoto A. An evolving automaton for RNA secondary structure prediction. In International Joint Conference on Neural Networks 2006, IJCNN '06. 2006. p. 2226-2233. 1716388. (IEEE International Conference on Neural Networks - Conference Proceedings).
Del Carpio, Carlos A.M. ; Ismael, Mohamed ; Ichiishi, Eichiro ; Koyama, Michihisa ; Kubo, Momoji ; Miyamoto, Akira. / An evolving automaton for RNA secondary structure prediction. International Joint Conference on Neural Networks 2006, IJCNN '06. 2006. pp. 2226-2233 (IEEE International Conference on Neural Networks - Conference Proceedings).
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