RNA Secondary Structure Analysis Using RNAstructure
نویسندگان
چکیده
منابع مشابه
RNAstructure: web servers for RNA secondary structure prediction and analysis
RNAstructure is a software package for RNA secondary structure prediction and analysis. This contribution describes a new set of web servers to provide its functionality. The web server offers RNA secondary structure prediction, including free energy minimization, maximum expected accuracy structure prediction and pseudoknot prediction. Bimolecular secondary structure prediction is also provide...
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Using a rigorous mathematical analysis, the prediction of RNA secondary structure as a function of free energy is obtained. The iterative method effectively allows a search over the entire configuration space of the RNA molecule not possible by earlier methods. The approach also allows for the direct inclusion of the nearest neighbor or stacking energies.
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Algorithms for prediction of RNA secondary structure— the set of base pairsthat form when an RNA molecule folds— are valuable to biologists who aim tounderstand RNA structure and function. Improving the accuracy and efficiencyof prediction methods is an ongoing challenge, particularly for pseudoknottedsecondary structures, in which base pairs overlap. This challenge is biologica...
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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...
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ژورنال
عنوان ژورنال: Current Protocols in Bioinformatics
سال: 2006
ISSN: 1934-3396,1934-340X
DOI: 10.1002/0471250953.bi1206s13