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Improved Covariance Model Parameter Estimation Using Rna Thermodynamic Properties, Jennifer A. Smith, Kay C. Wiese
Improved Covariance Model Parameter Estimation Using Rna Thermodynamic Properties, Jennifer A. Smith, Kay C. Wiese
Jennifer A. Smith
Covariance models are a powerful description of non-coding RNA (ncRNA) families that can be used to search nucleotide databases for new members of these ncRNA families. Currently, estimation of the parameters of a covariance model (state transition and emission scores) is based only on the observed frequencies of mutations, insertions, and deletions in known ncRNA sequences. For families with very few known members, this can result in rather uninformative models where the consensus sequence has a good score and most deviations from consensus have a fairly uniform poor score. It is proposed here to combine the traditional observed-frequency information with …