The affix array data structure and its applications to RNA secondary structure analysis
نویسندگان
چکیده
منابع مشابه
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15 صفحه اولRNA Secondary Structure: A Complete Mathematical Analysis
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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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...
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ژورنال
عنوان ژورنال: Theoretical Computer Science
سال: 2007
ISSN: 0304-3975
DOI: 10.1016/j.tcs.2007.09.029