The real and synthetic structured RNA benchmarks.

The real positive alignments are Rfam seed alignments. The synthetic alignments were generated using the program R-scape-sim from the Rfam positives; synthetic positives follow the phylogeny and preserve the secondary structure of the RNA family; synthetic decoys only preserve the phylogeny. The R-scape null decoys are the null alignments generated by R-scape and saved using the option --outnull. Details of all the alignments (such as length and average percentage identity) and their associated structures (number of base pairs, helices and helix length) are given in S1 Fig.