text: In the database, the information of the secondary structure and the primary sequence, represented by the MSA, is combined in statistical models called profile stochastic context-free grammars (SCFGs), also known as covariance models.  These are analogous to hidden Markov models used for protein family annotation in the Pfam database. Each family in the database is represented by two multiple sequence alignments in Stockholm format and a SCFG.
  The first MSA is the "seed" alignment.  It is a hand-curated alignment that contains representative members of the ncRNA family and is annotated with structural information.  This seed alignment is used to create the SCFG, which is used with the Rfam software INFERNAL to identify additional family members and add them to the alignment.  A family-specific threshold value is chosen to avoid false positives.
  Until release 12, Rfam used an initial BLAST filtering step because profile SCFGs were too computationally expensive. However, the latest versions of INFERNAL are fast enough so that the BLAST step is no longer necessary.
  The second MSA is the “full” alignment, and is created as a result of a search using the covariance model against the sequence database.  All detected homologs are aligned to the model, giving the automatically produced full alignment.