dorsal/arxiv
View SchemaPrediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations
| Authors | A. Xayaphoummine, T. Bucher, F. Thalmann, H. Isambert |
|---|---|
| Categories | |
| ArXiv ID | physics/0309117 |
| URL | https://arxiv.org/abs/physics/0309117 |
| DOI | 10.1073/pnas.2536430100 |
| Journal | Proceedings of the National Academy of Sciences USA 100 (2003) 15310-15315 |
Abstract
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on an O(n^2) clustering algorithm which computes time averages over a continously updated set of n reference structures. Applying this exact stochastic clustering approach, we typically obtain a 5- to 100-fold simulation speed-up for RNA sequences up to 400 bases, while the effective acceleration can be as high as 100,000-fold for short multistable molecules (<150 bases). We performed extensive folding statistics on random and natural RNA sequences, and found that pseudoknots are unevenly distributed amongst RNAstructures and account for up to 30% of base pairs in G+C rich RNA sequences (Online RNA folding kinetics server including pseudoknots : http://kinefold.u-strasbg.fr/ ).
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"abstract": "Ab initio RNA secondary structure predictions have long dismissed helices\ninterior to loops, so-called pseudoknots, despite their structural importance.\nHere, we report that many pseudoknots can be predicted through long time scales\nRNA folding simulations, which follow the stochastic closing and opening of\nindividual RNA helices. The numerical efficacy of these stochastic simulations\nrelies on an O(n^2) clustering algorithm which computes time averages over a\ncontinously updated set of n reference structures. Applying this exact\nstochastic clustering approach, we typically obtain a 5- to 100-fold simulation\nspeed-up for RNA sequences up to 400 bases, while the effective acceleration\ncan be as high as 100,000-fold for short multistable molecules (\u003c150 bases). We\nperformed extensive folding statistics on random and natural RNA sequences, and\nfound that pseudoknots are unevenly distributed amongst RNAstructures and\naccount for up to 30% of base pairs in G+C rich RNA sequences (Online RNA\nfolding kinetics server including pseudoknots : http://kinefold.u-strasbg.fr/\n).",
"arxiv_id": "physics/0309117",
"authors": [
"A. Xayaphoummine",
"T. Bucher",
"F. Thalmann",
"H. Isambert"
],
"categories": [
"physics.bio-ph",
"cond-mat.stat-mech",
"q-bio.BM"
],
"doi": "10.1073/pnas.2536430100",
"journal_ref": "Proceedings of the National Academy of Sciences USA 100 (2003)\n 15310-15315",
"title": "Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations",
"url": "https://arxiv.org/abs/physics/0309117"
},
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