random generation of rna secondary structures according to native distributions随机产生的rna二级结构根据原生分布.pdfVIP

Nebel et al. Algorithms for Molecular Biology 2011, 6:24 /content/6/1/24 RESEARCH Open Access Random generation of RNA secondary structures according to native distributions * Markus E Nebel, Anika Scheid and Frank Weinberg * Correspondence: a_scheid@cs. Abstract uni-kl.de Department of Computer Science, Background: Random biological sequences are a topic of great interest in genome University of Kaiserslautern, Germany analysis since, according to a powerful paradigm, they represent the background noise from which the actual biological information must differentiate. Accordingly, the generation of random sequences has been investigated for a long time. Similarly, random object of a more complicated structure like RNA molecules or proteins are of interest. Results: In this article, we present a new general framework for deriving algorithms for the non-uniform random generation of combinatorial objects according to the encoding and probability distribution implied by a stochastic context-free grammar. Briefly, the framework extends on the well-known recursive method for (uniform) random generation and uses the popular framework of admissible specifications of combinatorial classes, introducing weighted combinatorial classes to allow for the non-uniform generation by means of unranking. This framework is used to derive a