Approximation Scheme for RNA Structure Prediction Based on Base Pair Stacking
نویسندگان
چکیده
Pseudoknotted RNA secondary structure prediction is an important problem in computational biology. Existing polynomial time algorithms have no performance guarantee or can handle only limited types of pseudoknots. In this paper for the general problem of pseudoknotted RNA secondary structure prediction, a polynomial time approximation scheme is presented to predict pseudoknotted RNA secondary structure by dynamic programming and branch-bound based on base pair stacking. Compared with existing polynomial time algorithm, it has exact approximation performance and can predict arbitrary pseudoknots. Key-Words: RNA; Secondary Structure; Pseudoknot; Algorithm; Approximation Scheme; Dynamic Programming
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