منابع مشابه
The RNA shapes studio
MOTIVATION Abstract shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable to focusing in a single structure of minimal free energy. We report recent extensions to this approach. RESULTS We have rebuilt the original RNAshapes as a repository of components that allows us to integrate several established to...
متن کاملRelation Between RNA Sequences, Structures, and Shapes via Variation Networks
Background: RNA plays key role in many aspects of biological processes and its tertiary structure is critical for its biological function. RNA secondary structure represents various significant portions of RNA tertiary structure. Since the biological function of RNA is concluded indirectly from its primary structure, it would be important to analyze the relations between the RNA sequences and t...
متن کاملAbstract shapes of RNA.
The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of great interest, and efficient solutions based on thermodynamic parameters are known. Frequently, however, the predicted minimum free energy structures are not the native ones, leading to the necessity...
متن کاملrelation between rna sequences, structures, and shapes via variation networks
background: rna plays key role in many aspects of biological processes and its tertiary structure is critical for its biological function. rna secondary structure represents various significant portions of rna tertiary structure. since the biological function of rna is concluded indirectly from its primary structure, it would be important to analyze the relations between the rna sequences and t...
متن کاملShapes of topological RNA structures.
A topological RNA structure is derived by fattening the edges of a contact structure into ribbons. The shape of a topological RNA structure is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one, as well as isolated vertices. A shape contains the key topological information of the molecular conformation and for fixed topological genus there...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2014
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btu649