inference of RNA secondary structural alignments

 Infernal ("INFERence of RNA ALignment") searches DNA sequence
 databases for RNA structure and sequence similarities. It provides an
 implementation of a special variant of profile stochastic context-free
 grammars called covariance models (CMs). A CM is like a sequence
 profile, but it scores a combination of sequence consensus and RNA
 secondary structure consensus, so in many cases, it is more capable of
 identifying RNA homologs that conserve their secondary structure more
 than their primary sequence.
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 The tool is an integral component of the Rfam database.