Current Bioinformatics

Yi-Ping Phoebe Chen
Department of Computer Science and Information Technology
La Trobe University
Melbourne
Australia

Back

Recent Advances in RNA Secondary Structure Prediction with Pseudoknots

Author(s): Tatsuya Akutsu.

Abstract:

It has recently been recognized that pseudoknots of RNAs have important roles and not a small number of RNAs contain pseudoknots. Therefore, recent studies on RNA secondary structure prediction focus on pseudoknots. Several algorithms have been developed based on dynamic programming. Though optimality of a solution is guaranteed, these algorithms suffer from high time complexities. Thus, heuristic algorithms have also been developed, some of which are supposed to produce near optimal solutions in reasonable CPU time. Recently, another approach based on comparative modeling has been proposed. Several practical programs and web-based server programs are also developed based on the above-mentioned algorithms. The purpose of this review paper is to introduce the basic ideas in important algorithms for RNA secondary structure prediction with pseudoknots. This paper also tries to reveal relations among important algorithms.

Keywords: RNA secondary structure, pseudoknot, dynamic programming, structure prediction, RNA sequence

Order Reprints Order Eprints Rights & PermissionsPrintExport

Article Details

VOLUME: 1
ISSUE: 2
Year: 2006
Page: [115 - 129]
Pages: 15
DOI: 10.2174/157489306777011996
Price: $58