RNA Structure Determination from Sequence Alignment

Two of our projects (called KNetFold and CorreLogo) analyze sequence alignments with respect to potential conserved RNA secondary structure elements. One key concept is to use compensatory base changes in an alignment: these are correlated mutations that are consistent with Watson-Crick base pairings (for example the simultaneous mutation of an AU nucleotide pair in one sequence to a GC base pair in another se-quence). The compensatory base changes can indicate a conserved RNA base pair.