Expected degree for RNA secondary structure networks
نویسندگان
چکیده
منابع مشابه
Expected degree for RNA secondary structure networks
Consider the network of all secondary structures of a given RNA sequence, where nodes are connected when the corresponding structures have base pair distance one. The expected degree of the network is the average number of neighbors, where average may be computed with respect to the either the uniform or Boltzmann probability. Here, we describe the first algorithm, RNAexpNumNbors, that can comp...
متن کاملImproved RNA secondary structure prediction by maximizing expected pair accuracy.
Free energy minimization has been the most popular method for RNA secondary structure prediction for decades. It is based on a set of empirical free energy change parameters derived from experiments using a nearest-neighbor model. In this study, a program, MaxExpect, that predicts RNA secondary structure by maximizing the expected base-pair accuracy, is reported. This approach was first pioneer...
متن کاملExpected degree of finite preferential attachment networks
Abstract We provide an analytic expression for the quantity described in the title. Namely, we perform a preferential attachment growth process to generate a scale-free network. At each stage we add a new node with m new links. Let k denote the degree of a node, and N the number of nodes in the network. The degree distribution is assumed to converge to a power-law (for k ≥ m) of the form k and ...
متن کاملRNA secondary structure design.
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure we want to find a sequence that has a certain structure as its ground state. If such a sequence exists, the structure is called designable. We have implemented a branch-and-bound algorithm that is able to do an exhaustive search within the sequence space, i.e., gives an exact...
متن کاملRNA Secondary Structure Prediction.
In this unit, protocols are provided for predicting RNA secondary structure with the user-friendly RNAstructure desktop computer program and the RNAstructure Web server. The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented. © 2016 by Jo...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2014
ISSN: 0192-8651
DOI: 10.1002/jcc.23776