reducing the worst case running times of a family of rna and cfg problems, using valiants approach减少家庭的最坏情况运行时间的rna和cfg问题,使用的方法.pdfVIP

Zakov et al. Algorithms for Molecular Biology 2011, 6:20 /content/6/1/20 RESEARCH Open Access Reducing the worst case running times of a family of RNA and CFG problems, using Valiant’s approach * Shay Zakov, Dekel Tsur and Michal Ziv-Ukelson Abstract Background: RNA secondary structure prediction is a mainstream bioinformatic domain, and is key to computational analysis of functional RNA. In more than 30 years, much research has been devoted to defining different variants of RNA structure prediction problems, and to developing techniques for improving prediction quality. Nevertheless, most of the algorithms in this field follow a similar dynamic programming approach as that presented by Nussinov and Jacobson in the late 70’s, which typically yields cubic worst case running time algorithms. Recently, some algorithmic approaches were applied to improve the complexity of these algorithms, motivated by new discoveries in the RNA domain and by the need to efficiently analyze the increasing amount of accumulated genome-wide data. Results: We study Valiant’s classical algorithm for Context Free Grammar recognition in sub-cubic time, and extract features that are common to problems on which Valiant’s approach can be applied. Based on this, we describe several problem templates, and formulate generic algorithms that use Valiant’s technique and can be applied to all problems which abide by these templates, including many problems within the world of RNA Secondary Structures and Context Free Grammars. Conclusions: The algorithms presented in this paper improve the theoretical asymptotic worst case running time bounds for a large family of important problems. It is also possible that the suggested techniques could be applied to yield a practical speedup for