Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints


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… (More)
DOI: 10.1186/1471-2105-7-400

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