Target prediction and a statistical sampling algorithm for RNA-RNA interaction
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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 time and space algorithm is implemented in C (available from url{http://www.combinatorics.cn/cbpc/rip2.html})
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