The Detection and Assessment of Possible RNA Secondary Structure Using Multiple Sequence Alignment

We here devise a new method for detecting and assessing RNA secondary structure by using multiple sequence alignment. The central idea of the method is to first detect conserved stems in the alignment using a special matrix and then assess them by evaluating the ratio of the signal to the noise. We tested the method on data sets composed of pairwise and three-way alignments of known ncRNAs. For the pairwise tests, our method has sensitivity 61.42% and specificity 97.05% for structural alignments, and sensitivity 42.05% and specificity 98.15% for BLAST alignments. For the three-way tests, out method has sensitivity 65.17% and specificity 97.96% for structural alignments, and sensitivity 40.70% and specificity 97.87% for CLUSTALW alignments. Our method can detect conserved secondary structures in gapped or ungapped RNA alignments.