Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction?

Background: In ribonucleic acid (RNA) molecules whose function depends on their final, folded three-dimensional shape (such as those in ribosomes or spliceosome complexes), the secondary structure, defined by the set of internal basepair interactions, is more consistently conserved than the primary structure, defined by the sequence of nucleotides. Results: The research presented here investigates the possibility of applying a progressive, pairwise approach to the alignment of multiple RNA sequences by simultaneously predicting an energy-optimized consensus secondary structure. We take an existing algorithm for finding the secondary structure common to two RNA sequences, Dynalign, and alter it to align profiles of multiple sequences. We then explore the relative successes of different approaches to designing the tree that will guide progressive alignments of sequence profiles to create a multiple alignment and prediction of conserved structure. Conclusion: We have found that applying ...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Amelia B. Bellamy-Royds, Marcel Turcotte
• Keywords: BMCBI 2007, Ribonucleic Acid, Secondary Structure, Sequences