Fine-tuning structural RNA alignments in the twilight zone

Background: A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results: Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure align...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Andreas Bremges, Stefanie Schirmer, Robert Giegerich
• Keywords: BMCBI 2010, Multiple Sequence Alignment, Sequence Alignment, Twilight Zone