RNA analysis. Current automated approaches to analysing homologous RNA sequences and structures usually follow one of three "plans". Plan A uses aligned sequences (usually produced by a standard multiple sequence alignment algorithm) to infer a consensus secondary structure from the evolutionary and energetic information contained in an alignment. This is a highly successful approach, but is limited to data-sets with sequence homology high enough for the alignment step to work yet divergent enough for detection of structurally consistent mutations. Plan B employs the "Sankoff algorithm" to simultaneously align and infer a consensus structure. This algorithm requires extreme amounts of memory and time. Plan C aligns RNA structures rather than sequences. This approach can be used in the rare situation where reliable structures are known. Representative algorithms which could be used for each plan are indicated within the figure.
Gardner and Giegerich BMC Bioinformatics 2004 5:140 doi:10.1186/1471-2105-5-140