next up previous   Next: Future directions Up: Discussion Previous: Assessing the reliability

Merits of annotation of folding versus direct dotplot analysis

Although color annotation of a given folding provides an easy overview of many features and properties of a predicted folding, it does not substitute entirely for the direct examination of the dot plot output. In many instances more than one optimal folding is found for the same RNA sequence. Such structures are identified most readily in dot plots. It is also useful to examine close competing alternative structures in poorly determined regions of the plot. This is particularly useful when independent structural information is available that can be used to select likely structural candidates. Common structures in related RNA sequences are often found among suboptimal structure. Other types of auxilliary structural information can also often be used to identify likely suboptimal foldings in regions that are only moderately well determined.

Visual inspection of dot plots can also lead to the prediction of separate folding domains that do not interact with one another, as was the case in our analysis of the wild type Qβ genome [Jacobson & Zuker, 1993]. Color annotation on predicted structures does not tell us whether the alternative base pairs formed by bases in a particular domain are intra domain or extra domain. Only the dot plot can give us this information.

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