A New Algorithm for RNA Secondary Structure Design (2003)
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BibTeX
@MISC{Andronescu03anew,
author = {Mirela Andronescu and Anthony P. Fejes and Frank Hutter and Anne Condon and Holger H. Hoos and Department Of Microbiology},
title = {A New Algorithm for RNA Secondary Structure Design},
year = {2003}
}
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Abstract
The function of many RNAs crucially depends on their structure. Therefore, the design of RNA molecules with specific structural properties has many potential applications, e.g.,in the context of investigating the function of biological RNAs, of creating new ribozymes, or of designing artificial RNA nanostructures. Here, we present a new algorithm for solving the following RNA secondary structure design problem: Given a secondary structure, find an RNA sequence (if any) that is predicted to fold to that structure. Unlike the (pseudoknotfree) secondary structure prediction problem, this problem appears to be computationally hard. Our new algorithm, "RNA Secondary Structure Designer (RNA-SSD)", is based on stochastic local search, a prominent general approach for solving hard combinatorial problems. A thorough empirical...
