Many functional RNAs have evolutionarily conserved secondary
structures, and conserved RNA base pairing induces strong pairwise
sequence correlations between the interacting positions in RNA
multiple sequence alignments. This distinctive and powerful
statistical signal can be exploited in many kinds of comparative
genome sequence analysis of structural RNAs, including structure-based
homology searches, RNA sequence alignment, consensus RNA structure
prediction, and computational genomic screens for new RNAs.