Motivation: RNA family models group nucleotide sequences that share a common biological function. These models can be used to find new sequences belonging to the same family. To succeed in this task, a model needs to exhibit high sensitivity as well as high specificity. As model construction is guided by a manual process, a number of problems can occur, such as the introduction of more than one model for the same family or poorly constructed models. We explore the Rfam database to discover such problems. Results: Our main contribution is in the definition of the discriminatory power of RNA family models, together with a first algorithm for its computation. In addition, we present calculations across the whole Rfam database that show several families lacking high specificity when compared to other families. We give a list of these clusters of families and provide a tentative explanation. Our program can be used to: (i) make sure that new models are not equivalent to any model already present in the database; and (ii) new models are not simply submodels of existing families. Availability: www.tbi.univie.ac.at/software/cmcompare/. The code is licensed under the GPLv3. Results for the whole Rfam database and supporting scripts are available together with the software.

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