Sciweavers

Share
CIBCB
2009
IEEE

rnaDesign: Local search for RNA secondary structure design

9 years 6 months ago
rnaDesign: Local search for RNA secondary structure design
Abstract-- The RNA secondary structure design (SSD) problem is a recently emerging research topic motivated by applications such as customized drug design and the self-assembly of RNA nano-objects. This paper presents a novel local search algorithm, rnaDesign for SSD solving. An evaluation of the algorithm performance in terms of sequence affinity and structure specificity is made through comparison with another algorithm, RNAinverse. Experiments were performed on RNA secondary structures including three biologically existing data sets and one random structure set. Empirical results show that rnaDesign outperforms RNAinverse in terms of structure designability; sequences designed by rnaDesign also exhibit better thermodynamic stability with relatively lower folding energy. Furthermore, we demonstrate through parameter tuning experiments that using a combination of heuristic search strategies leads to better design performance; there also exists a strong correlation between the heuristi...
Denny C. Dai, Herbert H. Tsang, Kay C. Wiese
Added 08 Nov 2010
Updated 08 Nov 2010
Type Conference
Year 2009
Where CIBCB
Authors Denny C. Dai, Herbert H. Tsang, Kay C. Wiese
Comments (0)
books