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 - 2006 Dec 1
EventInternational Joint Conference on Neural Networks 2006, IJCNN '06 - Vancouver, BC, Canada
Duration: 2006 Jul 162006 Jul 21

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
Period06/7/1606/7/21

ASJC Scopus subject areas

  • Software

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  • 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).