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• W2951921618 abstract "Summary: Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics- based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary structures. As a showcase application for this new feature of the ViennaRNA Package we compare three distinct, previously published strategies to utilize SHAPE reactivities for structure prediction. The new tool is benchmarked on a set of RNAs with known reference structure. Availability and implementation: The capability for SHAPE directed RNA folding is part of the upcoming release of the ViennaRNA Package 2.2, for which a preliminary release is already freely available at http://www.tbi.univie.ac.at/RNA." @default.
• W2951921618 created "2019-06-27" @default.
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• W2951921618 date "2015-02-20" @default.
• W2951921618 modified "2023-09-27" @default.
• W2951921618 title "SHAPE directed RNA folding" @default.
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• W2951921618 doi "https://doi.org/10.1101/015537" @default.
• W2951921618 hasPublicationYear "2015" @default.
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