Rfam

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From the Rfam web page:

"Rfam is a collection of multiple sequence alignments and covariance models covering many common non-coding RNA families."

It is similar to Pfam, which contains profile hidden Markov models for protein annotation, used by HMMER for annotating protein sequences. Similarly, the Infernal package is used in conjunction with Rfam for searching for RNA motifs using convariance models.

The current Rfam database can be found at two locations:

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