Target prediction and a statistical sampling algorithm for RNA-RNA interaction

2009/08/05 by F. W. D. Huang, Fenix W. D. Huang, Huang, F. W. D. +9
Biochemistry, Genetics and Molecular Biology · Mathematics · #05A16 #Biomolecules (q-bio.BM) #Combinatorics (math.CO) #FOS: Biological sciences #FOS: Mathematics #Quantitative Methods (q-bio.QM) #RNA Research and Splicing #RNA and protein synthesis mechanisms #RNA modifications and cancer #Statistics Theory (math.ST) #math.CO #math.ST #msc:05A16 #q-bio.BM #q-bio.QM #stat.TH

paper · pdf · doi:10.48550/arxiv.0908.0597

7 pages, 10 figures

arxiv created 2009/08/05 · openalex publication_date 2009/08/05 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

It has been proven that the accessibility of the target sites has a critical influence for miRNA and siRNA. In this paper, we present a program, rip2.0, not only the energetically most favorable targets site based on the hybrid-probability, but also a statistical sampling structure to illustrate the statistical characterization and representation of the Boltzmann ensemble of RNA-RNA interaction structures. The outputs are retrieved via backtracing an improved dynamic programming solution for the partition function based on the approach of Huang et al. (Bioinformatics). The O(N⁶) time and O(N⁴) space algorithm is implemented in C (available from \urlhttp://www.combinatorics.cn/cbpc/rip2.html)

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