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Discussion

We have described several new computer programs that have been designed to enable the user to determine the reliability of predicted RNA secondary structures relatively easily. Colored dots are used to provide a simple overview of how well determined an entire predicted structure and/or a predicted structural domain within a larger folding is. Although the same information can be obtained from dot plot representations of optimal and suboptimal foldings that is created both by mfold and by the Vienna package, the dot plot representation of RNA secondary structures is relatively difficult to understand. In addition, it is sometimes difficult to integrate information in the dot plots accurately by eye. Thus the use of color is helpful even to an experienced user.

• Assessing the reliability of a prediction
• Merits of annotation of folding versus direct dotplot analysis
• Future directions
• Methods

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Michael Zuker Institute for Biomedical Computing Washington University in St. Louis August 21 1998.