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Article information
2000 , Volume 5, Special issue, p.48-56
Titov I.I., Ivanisenko V.A., Kolchanov N.A.
Fitness - a WWW-resource for RNA folding simulation based on genetic algorithm with local minimization
Genetic algorithm is a promising method for RNA secondary structure prediction, combining the value of an effective minimization tool, the possibility to search for intermediate RNA folding states and the freedom in folding rules, e.g. an account for pseudo-knots. Existing nowadays genetic algorithms for secondary structure calculation are not fast enough for their use via Internet. This work presents a web-resource for RNA secondary structure prediction on the basis of genetic algorithm. Optimization speed and quality are obtained through combination of global search and local minimization, as well as by an effective sampling of the structure space with initial population and algorithm parameters optimization. Besides the RNA secondary structure prediction it can simulate its refolding under the influence of an antisense nucleotide. This feature can be useful for gene-directed drug design.
Author(s):
Titov I.I.
Office: Institute of Cytology and Genetics SB RAS
Address: Russia, Novosibirsk
E-mail: titov@bionet.nsc.ru
Ivanisenko V.A.
PhD.
Office: Institute of Cytology and Genetics SB RAS
Address: Russia, Novosibirsk
E-mail: titov@bionet.nsc.ru
Kolchanov N.A.
Office: Institute of Cytology and Genetics SB RAS
Address: Russia, Novosibirsk
Bibliography link:
Titov I.I., Ivanisenko V.A., Kolchanov N.A. Fitness - a WWW-resource for RNA folding simulation based on genetic algorithm with local minimization // Computational technologies. 2000. V. 5. The special issue is devoted to the 10-th anniversary of the Laboratory of Theoretical Genetics of the Institute of Cytology and Genetics SB RAS. P. 48-56
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