On The Dangers Of Aligning RNA Sequences Using “Conserved” Motifs

Abstract

Aligning RNA sequences can be a challenging task. Automatic sequence alignment programs typically align sequences only with respect to primary sequence, and as a result may yield spurious alignments. Incorporating information on RNA secondary structure can improve the alignment, but this must usually be done by hand. One approach to aligning RNA sequences uses "conserved motifs", however relying on these motifs may lead to gross errors of alignment if, in fact, those motifs are not conserved.