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Nucleic Acids Research, 2000, Vol. 28, No. 4 991-999
© 2000 Oxford University Press

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

Jih-H. Chen*, Shu-Yun Le1 and Jacob V. Maizel1

Advanced Biomedical Computing Center, SAIC, NCI/FCRDC, Frederick, MD 21702, USA and 1Laboratory of Experimental and Computational Biology, National Cancer Institute, Frederick Cancer Research and Development Center, National Institutes of Health, Building 469, Room 151, Frederick, MD 21702, USA

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.

* To whom correspondence should be addressed. Tel: +1 301 846 5773; Fax: +1 301 846 5762; Email: chen@ncifcrf.gov


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