[8][9][10] The INFERNAL package can also be used with Rfam to annotate sequences (including complete genomes) for homologues to known ncRNAs.

These are analogous to hidden Markov models used for protein family annotation in the Pfam database.

It is a hand-curated alignment that contains representative members of the ncRNA family and is annotated with structural information.

Until release 12, Rfam used an initial BLAST filtering step because profile SCFGs were too computationally expensive.

[11] The second MSA is the “full” alignment, and is created as a result of a search using the covariance model against the sequence database.