Document Detail

Determinants of simulated RNA evolution.
MedLine Citation:
PMID:  16098538     Owner:  NLM     Status:  MEDLINE    
Models of RNA secondary structure folding are widely used to study evolution in theory and simulation. However, systematic studies of the parameters involved are rare. In this paper, we study by simulation how RNA evolution is influenced by three different factors, namely the mutation rate, scaling of the fitness function, and distance measure. We found that for low mutation rates the qualitative evolutionary behavior is robust with respect to the scaling of the fitness function. For efficient mutation rates, which are close to the error threshold, scaling and distance measure have a strong influence on the evolutionary behavior. A global distance measure that takes sequence information additively into account lowers the error threshold. When using a local sequence-structure alignment for the distance, we observed a smoother evolution of the fitness over time. Finally, in addition to the well known error threshold, we identify another threshold of the mutation rate, called divergence threshold, where the qualitative transient behavior changes from a localized to an exploratory search.
Anne Kupczok; Peter Dittrich
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2005-08-11
Journal Detail:
Title:  Journal of theoretical biology     Volume:  238     ISSN:  0022-5193     ISO Abbreviation:  J. Theor. Biol.     Publication Date:  2006 Feb 
Date Detail:
Created Date:  2006-01-17     Completed Date:  2006-05-03     Revised Date:  2009-11-19    
Medline Journal Info:
Nlm Unique ID:  0376342     Medline TA:  J Theor Biol     Country:  England    
Other Details:
Languages:  eng     Pagination:  726-35     Citation Subset:  IM    
Bio Systems Analysis Group, Jena Centre for Bioinformatics and Department of Mathematics and Computer Science, Friedrich Schiller University Jena, D-07743 Jena, Germany.
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MeSH Terms
Computer Simulation*
Evolution, Molecular*
Models, Genetic*
Nucleic Acid Conformation
RNA / genetics*
Selection, Genetic
Sequence Alignment
Reg. No./Substance:

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