DrTransformer: Heuristic cotranscriptional RNA folding using the nearest neighbor energy model
- Creators
- Badelt, Stefan
- Lorenz, Ronny
- Hofacker, Ivo L.
Abstract
Background. Folding during transcription can have an important influence on the structure and function of ℝNA molecules, as regions closer to the 5' end can fold into metastable structures before potentially stronger interactions with the 3' end become available. Thermodynamic ℝNA folding models are not suitable to analyze this problem, as they can only calculate properties of the equilibrium distribution. Other software packages that simulate the kinetic process of ℝNA folding during transcription exist, but they are mostly applicable for short sequences. Results. We present a new algorithm that tracks changes to the ℝNA secondary structure ensemble during transcription. At every transcription step, new representative local minima are identified, a neighborhood relation is defined and transition rates are estimated for kinetic simulations. After every simulation, a part of the ensemble is removed and the remainder is used to search for new potentially relevant structures. The presented algorithm is deterministic (up to numeric instabilities of simulations), fast (in comparison with existing methods), and it is capable of folding ℝNAs much longer than 200 nucleotides. Availability This software is open-source and available at https://github.com/ViennaRNA/drtransformer.
Additional Information
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. We thank Christoph Flamm, Andrea Tanzer, and Michael T. Wolfinger for fruitful discussions in the early stages of the development of DrTransformer. SB wants to thank Erik Winfree for inspiring discussions on kinetic models for nucleic acid folding. This work was supported in part by grants from the Austrian Science Foundation (FWF), grant numbers F 80 to ILH and I 4520 to RL. SB was funded by the Austrian DK RNA program FG748004, the Caltech Biology and Biological Engineering Division Fellowship and the NSF Grant No. 1643606: Computational Parameterization of Nucleic Acid Secondary Structure Models. The authors have declared no competing interest.Attached Files
Submitted - 2022.09.08.507181v1.full.pdf
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Additional details
- Eprint ID
- 120335
- Resolver ID
- CaltechAUTHORS:20230322-367275000.20
- F 80
- FWF Der Wissenschaftsfonds
- I 4520
- FWF Der Wissenschaftsfonds
- W 1207
- FWF Der Wissenschaftsfonds
- Caltech Division of Biology and Biological Engineering
- CHE-1643606
- NSF
- Created
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2023-03-28Created from EPrint's datestamp field
- Updated
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2023-03-28Created from EPrint's last_modified field