Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.
MOTIVATION: Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods, however, ignore biophysical factors, such as the kinetics of RNA folding; no current im...
| Main Authors: | , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
2013
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| _version_ | 1826293166146322432 |
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| author | Anderson, J Haas, P Mathieson, L Volynkin, V Lyngsø, R Tataru, P Hein, J |
| author_facet | Anderson, J Haas, P Mathieson, L Volynkin, V Lyngsø, R Tataru, P Hein, J |
| author_sort | Anderson, J |
| collection | OXFORD |
| description | MOTIVATION: Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods, however, ignore biophysical factors, such as the kinetics of RNA folding; no current implementation considers both evolutionary information and folding kinetics, thus losing information that, when considered, might lead to better predictions. RESULTS: We present an iterative algorithm, Oxfold, in the framework of stochastic context-free grammars, that emulates the kinetics of RNA folding in a simplified way, in combination with a molecular evolution model. This method improves considerably on existing grammatical models that do not consider folding kinetics. Additionally, the model compares favourably to non-kinetic thermodynamic models. |
| first_indexed | 2024-03-07T03:25:54Z |
| format | Journal article |
| id | oxford-uuid:b90653ca-9403-4a07-84a5-6211b46cb423 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T03:25:54Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | oxford-uuid:b90653ca-9403-4a07-84a5-6211b46cb4232022-03-27T05:00:06ZOxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:b90653ca-9403-4a07-84a5-6211b46cb423EnglishSymplectic Elements at Oxford2013Anderson, JHaas, PMathieson, LVolynkin, VLyngsø, RTataru, PHein, J MOTIVATION: Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods, however, ignore biophysical factors, such as the kinetics of RNA folding; no current implementation considers both evolutionary information and folding kinetics, thus losing information that, when considered, might lead to better predictions. RESULTS: We present an iterative algorithm, Oxfold, in the framework of stochastic context-free grammars, that emulates the kinetics of RNA folding in a simplified way, in combination with a molecular evolution model. This method improves considerably on existing grammatical models that do not consider folding kinetics. Additionally, the model compares favourably to non-kinetic thermodynamic models. |
| spellingShingle | Anderson, J Haas, P Mathieson, L Volynkin, V Lyngsø, R Tataru, P Hein, J Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title | Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title_full | Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title_fullStr | Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title_full_unstemmed | Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title_short | Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title_sort | oxfold kinetic folding of rna using stochastic context free grammars and evolutionary information |
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