Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints |
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Authors: | Robin D Dowell and Sean R Eddy |
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Institution: | (1) Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd, Box 8510, St. Louis, MO 63108, USA;(2) MIT Computer Science and Artificial Intelligence Laboratory, , 32 Vassar Street, Cambridge, MA 02139, USA |
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Abstract: | Background We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited
comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment
is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good
unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational
complexity of the algorithm. |
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Keywords: | |
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