منابع مشابه
Combinatorics on Plane Trees, Motivated by RNA Secondary Structure Configurations
Motivated by the base pairing of RNA sequences, and as part of our collaboration with A. Condon and H. H. Hoos, we defined the local move operation on two unobstructed edges in a plane tree given here. We now consider the graph Gn induced by this operation on Tn, the set of plane trees with n edges. We provide a series of results showing that Gn is a connected, n-partite graph of diameter n− 1 ...
متن کاملLinear Time Algorithm for Parsing RNA Secondary Structure
Accurate prediction of pseudoknotted RNA secondary structure is an important computational challenge. Typical prediction algorithms aim to find a structure with minimum free energy according to some thermodynamic (“sum of loop energies”) model that is implicit in the recurrences of the algorithm. However, a clear definition of what exactly are the loops and stems in pseudoknotted structures, an...
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 کاملRna Secondary Structure Prediction
Understanding secondary structures of RNAs helps to determine their chemical and biological properties. Only a small number of RNA structures have been determined currently since such structure determination experiments are timeconsuming and expensive. As a result, scientists start to rely on RNA secondary structure prediction. Unlike protein structure prediction, predicting RNA secondary struc...
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ژورنال
عنوان ژورنال: Discrete Applied Mathematics
سال: 1994
ISSN: 0166-218X
DOI: 10.1016/0166-218x(92)00038-n