Title: Simultaneous alignment and structure prediction of three RNA sequences

Authors: Beeta Masoumi, Marcel Turcotte

Addresses: School of Information Technology and Engineering, University of Ottawa, 800 King Edward, Ottawa, Ontario, K1N 6N5, Canada. ' School of Information Technology and Engineering, University of Ottawa, 800 King Edward, Ottawa, Ontario, K1N 6N5, Canada

Abstract: 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.

Keywords: RNA sequences; secondary structure; sequence alignment; dynamic programming; bioinformatics; structure prediction; free energy minimisation; comparative sequence analysis; minimum free energy structure.

DOI: 10.1504/IJBRA.2005.007581

International Journal of Bioinformatics Research and Applications, 2005 Vol.1 No.2, pp.230 - 245

Published online: 06 Aug 2005 *

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