Rfam: updates to the RNA families database

Gardner, Paul P.; Daub, Jennifer; Tate, John G.; Nawrocki, Eric P.; Kolbe, Diana L.; Lindgreen, Stinus; Wilkinson, Adam C.; Finn, Robert D.; Griffiths-Jones, Sam; Eddy, Sean R.; Bateman, Alex

In order to improve the species and sequence depth of individual Rfam families, more than 370 families have been expanded by an 'iteration' process, in which some sequences in the FULL alignment are chosen for promotion to the SEED alignment. The sequences selected from FULL alignments for inclusion in the SEED must pass a series of stringent quality control requirements and be manually approved by a curator. The quality control steps include: ensuring that the sequence and secondary structure are consistent with the existing SEED sequences; the sequence identity with existing SEED sequences falls within 60-95%; the sequence is not truncated with respect to the SEED alignment. The curator also ensures that the new sequences make phylogenetic sense before allowing them to be incorporated into an updated SEED. An example of the utility of iteration is the snoRNA U103 SEED from Rfam 8.1 (accession: RF00188), which contained just three sequences and spanned two eutherian mammals (human and mouse). The SEED in Rfam 9.0 after iteration contains 42 sequences and spans Eutheria, Teleost (ray-finned fishes), Iguanidae, Monotremes, Marsupials, Placentals, Aves and Chondrichthyes (cartilaginous fishes).