Rfam covariance model alignment
Covariance models from Rfam are aligned to genomes in Ensembl Plants and Ensembl Metazoa. The covariance models are taxonomically filtered before alignment, so that structural RNA features that have never been annotated in plant species are not inappropriately aligned. The alignment is performed with cmscan, from the Infernal software suite.
The Rfam alignments are visible as a browser track (named 'Rfam models'); selecting an alignment in the genome browser displays metadata such as the Rfam description and the secondary structure.
These alignments form the basis of the main component of RNA gene annotation in Ensembl Genomes.