rna accessibility in cubic timerna在立方时间可访问性.pdfVIP

Bernhart et al. Algorithms for Molecular Biology 2011, 6:3 /content/6/1/3 RESEARCH Open Access RNA Accessibility in cubic time * Stephan H Bernhart , Ullrike Mückstein, Ivo L Hofacker Abstract Background: The accessibility of RNA binding motifs controls the efficacy of many biological processes. Examples are the binding of miRNA, siRNA or bacterial sRNA to their respective targets. Similarly, the accessibility of the Shine-Dalgarno sequence is essential for translation to start in prokaryotes. Furthermore, many classes of RNA binding proteins require the binding site to be single-stranded. 3 Results: We introduce a way to compute the accessibility of all intervals within an RNA sequence in O (n ) time. This improves on previous implementations where only intervals of one defined length were computed in the same time. While the algorithm is in the same efficiency class as sampling approaches, the results, especially if the probabilities get small, are much more exact. Conclusions: Our algorithm significantly speeds up methods for the prediction of RNA-RNA interactions and other applications that require the accessibility of RNA molecules. The algorithm is already available in the program RNAplfold of the ViennaRNA package. Background intermolecular duplex δGint and the cost of opening the The importance of RNA within living cells has been rea- binding sites δGopen. The opening energy can be com- lized in the last two decades. RNA provides a layer of puted from the accessibility, defined as the probability regulation in eukaryotes, e.g.