Simultaneous alignment and structure prediction of three RNA sequences.

Comparative RNA sequence analyses have contributed remarkably accurate predictions. The recent determination of the 30S and 50S ribosomal subunits bringing more supporting evidence. Several inference tools are combining free energy minimisation and comparative analysis to improve the quality of secondary structure predictions. This paper investigates the following hypotheses: the use of three input sequences improves the average accuracy compared to predictions based on two input sequences; the worse prediction (minimum accuracy) for any sequence should be more accurate when three input sequences are used rather than two; finally, the consensus structure of three sequences is probably less representative of the individual sequences. The average coverage should be less.