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
    PublisherInstitute of Electrical and Electronics Engineers Inc.
    Pages2226-2233
    Number of pages8
    ISBN (Print)0780394909, 9780780394902
    DOIs
    Publication statusPublished - 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

    All Science Journal Classification (ASJC) codes

    • Software

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