ALIDOT (ALIgned DOT-plots) detects conserved secondary structure elements in relatively small sets of RNAs by combining multiple sequence alignments and secondary structure predictions. Both a (good) sequence alignment and predicted secondary structure predictions for each sequence in the alignment must be provided as inputs. alidot works either with predicted mfe structures, or with base pairing probability matrices.
The program alidot and the associated perl scripts are part of the Vienna RNA Package.
:: MORE INFORMATION
Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes
Ivo L. Hofacker and Peter F. Stadler
Comp & Chem., 23, 401-414 (1999)