Substitution-ranked ncRNA candidates

Selection and ranking

Based on a subset of the classes of the overall classification scheme, sets of ncRNA candidates, ranked by number of supporting substitutions, have been made.

Three sets (hairpins, Y-shaped, and clover-shaped) were made based on the intronic and intergenic long folds (more than 15 pairs). A score directly based on the observed substitutions (score = [#compensatory + 0.25*#compatible - 0.5*#contradictory]/pairs) were used to rank the folds. This presents an alternative to the log-odds score assigned by EvoFold, which favors deeply conserved compact folds. Only folds with less than 50% bulges in their stems were included. These ranked sets can be browsed or downloaded in bulk (format description) by following the links given in the tables below.