RNA Secondary Structure Analysis Using RNAstructure
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- Abstract
- Table of Contents
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- Literature Cited
Abstract
RNAstructure is a user?friendly program for the prediction and analysis of RNA secondary structure under Microsoft Windows. This unit provides protocols for RNA secondary structure prediction and prediction of high?affinity oligonucleotide binding sites to a structured RNA target.
Keywords: RNA Secondary Structure Prediction; Free Energy Minimization; Thermodynamics
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PDF or HTML at Wiley Online LibraryTable of Contents
- Basic Protocol 1: Predicting Secondary Structure and Predicting Base‐Pair Probabilities
- Basic Protocol 2: Predicting Binding Affinities of Oligonucleotides Complementary to an RNA Target with OligoWalk
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
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Figure 12.6.1 Screen shot of the RNAstructure sequence editor. The D. melanogaster 5S rRNA sequence is entered and formatted using the Format Sequence button. View Image -
Figure 12.6.2 Screen shot of the RNA secondary structure prediction window. View Image -
Figure 12.6.3 The lowest free energy secondary structure predicted for the D. melanogaster 5S rRNA sequence as drawn by RNAstructure. View Image -
Figure 12.6.4 The probability dot plot for base pairs in the D. melanogaster 5S rRNA sequence. Each dot in this plot is a single base pair and is associated with a base‐pairing probability. For pairs between nucleotides i and j , with i < j , i is down the right‐hand side of the plot and j is across the top. In RNAstructure, dots are colored to indicate a probability interval, with the most probable pairs in red and the least probable in blue. The current base pairs displayed have pairing probability of ≥1%. A color key is drawn at the bottom of the window (not shown in this view). After clicking on a dot, the pair and −log10 (base‐pair probability) are indicated at the bottom of the RNAstructure window. The current display shows that the base pair between G75 and C102 was clicked and has −log10 (base‐pair probability) of 5.33232 × 10−2 (88.4457%). View Image -
Figure 12.6.5 The lowest free energy secondary structure predicted for the D. melanogaster 5S rRNA sequence with color annotation. The color annotation key is shown in the lower right‐hand corner. The most probable base pairs are red and least probable are violet. The predicted pairs with the highest base pair probabilities are more likely to be correctly predicted pairs (Mathews, ). View Image -
Figure 12.6.6 The OligoWalk input window. View Image -
Figure 12.6.7 The OligoWalk output display. View Image
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Literature Cited
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| Internet Resources | |
| http://rna.urmc.rochester.edu | |
| Mathews lab Web site, where RNAstructure can be downloaded. |
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