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Rfam covariance model alignment

Covariance models from Rfam are aligned to genomes in Ensembl Plants (with other divisions to follow in future releases). 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.

See also: Non-coding RNA annotation.