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Prediction of common secondary structures of RNAs: a genetic algorithm approach

  1. Author:
    Chen, J. H.
    Le, S. Y.
    Maizel, J. V.

  2. Author Address

    Chen JH NCI, Frederick Canc Res & Dev Ctr, SAIC, Adv Biomed Comp Ctr Frederick, MD 21702 USA NCI, Frederick Canc Res & Dev Ctr, SAIC, Adv Biomed Comp Ctr Frederick, MD 21702 USA NCI, Frederick Canc Res & Dev Ctr, Lab Expt & Computat Biol, NIH Frederick, MD 21702 USA
    1. Year: 2000
  2. Journal: Nucleic Acids Research
    1. 28
    2. 4
    3. Pages: 991-999
  4. Type of Article: Article
  1. Abstract:

    In this study we apply a genetic algorithm to a set of RNA sequences to find common RNA secondary structures. Our method is a three-step procedure. At the first stage of the procedure for each sequence, a genetic algorithm is used to optimize the structures in a population to a certain degree of stability. In this step, the free energy of a structure is the fitness criterion for the algorithm. Next, for each structure, we define a measure of structural conservation with respect to those in other sequences. We use this measure in a genetic algorithm to improve the structural similarity among sequences for the structures in the population of a sequence. Finally, we select those structures satisfying certain conditions of structural stability and similarity as predicted common structures for a set of RNA sequences. We have obtained satisfactory results from a set of tRNA, 5S rRNA, rev response elements(RRE) of HIV-1 and RRE of HIV-2/SIV, respectively. [References: 22]

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