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RNA secondary structures: comparison and determination of frequently recurring substructures by consensus |
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| Authors: | Le Shu-Yun; Owens John; Nussinov Ruth; Chen Jih-H; Shapiro Bruce; Maizel Jacob V |
| Institution: | Laboratory of Mathematical Biology, Division of Cancer Biology and Diagnosis, National Cancer Institute, National Institutes of Health Bldg 469, Rm 151, Frederick, MD 21701, USA 1Shanghai Institute of Biochemistry, Chinese Academy of Sciences Shanghai 200031, China 2Sackler Institute for Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University Ramat Aviv, Israel 3Advanced Scientific Computer Laboratory, Program Resources, Inc. NCI/FCRF, Frederick, MD 21701, USA |
| Abstract: | A method for assessing the preserved stem - loops of RNA secondarystructures is presented. Frequently recurring helical stemsin a set of secondary structures resulting from the simulatedfolding process of a given RNA are assessed and consensus structuralmotifs can then be selected to construct a secondary structureof the RNA. Alternatively, it can be applied to a series of‘optimal’ and ‘suboptimal’ secondarystructures computed using the dynamic program developed by Williamsand Tinoco. To demonstrate the power and the usefulness of theprogram we give examples of this procedure. Received on October 28, 1987; accepted on April 2, 1989 |
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