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, our 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.
rna secondary structure multiple sequence alignment non-coding rna