Among the most powerful and commonly used methods for finding new members of non-coding RNA gene families in genomic data are covariance models. The parameters of these models are estimated from the observed position-specific frequencies of insertions, deletions, and mutations in a multiple alignment of known non-coding RNA family members. Since the vast majority of positions in the multiple alignment have no observed changes, yet there is no reason to rule them out, some form of prior is applied to the estimate. Currently, observed-frequency priors are generated from non-family members based on model node type and child node type allowing for some differentiation between priors for loops versus helices and between internal segments of structures and edges of structures. In this work it is shown that parameter estimates might be improved when thermodynamic data is combined with the consensus structure/sequence and observed-frequency priors to create more realistic position-specific priors.
Available at: http://works.bepress.com/jennifer_smith/21/