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WIREs RNA
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New insights from cluster analysis methods for RNA secondary structure prediction

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A widening gap exists between the best practices for RNA secondary structure prediction developed by computational researchers and the methods used in practice by experimentalists. Minimum free energy predictions, although broadly used, are outperformed by methods which sample from the Boltzmann distribution and data mine the results. In particular, moving beyond the single structure prediction paradigm yields substantial gains in accuracy. Furthermore, the largest improvements in accuracy and precision come from viewing secondary structures not at the base pair level but at lower granularity/higher abstraction. This suggests that random errors affecting precision and systematic ones affecting accuracy are both reduced by this ‘fuzzier’ view of secondary structures. Thus experimentalists who are willing to adopt a more rigorous, multilayered approach to secondary structure prediction by iterating through these levels of granularity will be much better able to capture fundamental aspects of RNA base pairing. WIREs RNA 2016, 7:278–294. doi: 10.1002/wrna.1334 This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA
The two Sfold cluster centroids for Agrobacterium tumefaciens 5S. The first is the minimum free energy (MFE) structure, the second very close to the native; they respectively represent clusters with probabilities 62.1 and 37.9%. Base pairs in the symmetric difference are shown in yellow and total 47. Base pairs separating the second from the native are shown in red; many are noncanonical. Note that single‐stranded bases do not count toward the symmetric difference.
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Median run time of Sfold, profiling, RNAshapes, and RNAHeliCes.
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Median number of groups for each RNA family. RNAHeliCes always by design returns three groups, and is included here for reference.
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Precision comparisons for representative structures (left) and signatures (right). Median scores are reported for each family. Sfold centroids are used for both. Neither RNAHeliCes nor the minimum free energy (MFE) prediction are included, since both are deterministic with perfect precision. Note the improvement in precision for signatures versus structures.
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Accuracy comparisons for representative structures (left) and signatures (right). Median scores are reported for each family. Sfold centroids are used for both. The median minimum free energy (MFE) F‐measure is also reported for comparison. Note the significant improvement in accuracy for signatures versus structures.
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Four VcQrr3 consensus structures, with colors indicating different features. Their probabilities are, clockwise from top left, 6.8, 56.4, 7.0, and 20.5% Each structure as a combination of colors illustrates profiling's representation of a structure as a set of features. The minimum free energy (MFE) structure is the lower left.
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The two alternating native structures for the spliced leader RNA from Leptomonas collosoma. Both have the same shape [], but different hishapes. The first structure has the innermost base pair (25, 29) and thus an index of ; its hishape is . The second structure has a helix midpoint of and a hishape of .
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The three shapes present in a Natronomonas pharaonis tRNA‐ala sample, with their shreps; their probabilities from left to right are 99.0, 0.7 and 0.3%. The minimum free energy (MFE) is the shrep for the first, most populous shape, while the native is the shrep for the last.
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