dorsal/arxiv
View SchemaA Statistical Analysis of RNA Folding Algorithms Through Thermodynamic Parameter Perturbation
| Authors | D. M. Layton, R. Bundschuh |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0411049 |
| URL | https://arxiv.org/abs/q-bio/0411049 |
Abstract
Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction algorithms are to changes in these parameters. We find that already for changes corresponding to the actual experimental error to which these parameters have been determined 30% of the structure are falsly predicted and the ground state structure is preserved under parameter perturbation in only 5% of all cases. We establish that base pairing probabilities calculated in a thermal ensemble are a viable though not perfect measure for the reliability of the prediction of individual structure elements. A new measure of stability using parameter perturbation is proposed, and its limitations discussed.
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"abstract": "Computational RNA secondary structure prediction is rather well established.\nHowever, such prediction algorithms always depend on a large number of\nexperimentally measured parameters. Here, we study how sensitive structure\nprediction algorithms are to changes in these parameters. We find that already\nfor changes corresponding to the actual experimental error to which these\nparameters have been determined 30% of the structure are falsly predicted and\nthe ground state structure is preserved under parameter perturbation in only 5%\nof all cases. We establish that base pairing probabilities calculated in a\nthermal ensemble are a viable though not perfect measure for the reliability of\nthe prediction of individual structure elements. A new measure of stability\nusing parameter perturbation is proposed, and its limitations discussed.",
"arxiv_id": "q-bio/0411049",
"authors": [
"D. M. Layton",
"R. Bundschuh"
],
"categories": [
"q-bio.QM",
"q-bio.BM"
],
"title": "A Statistical Analysis of RNA Folding Algorithms Through Thermodynamic Parameter Perturbation",
"url": "https://arxiv.org/abs/q-bio/0411049"
},
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