Author: Reeder, Jens; Steffen, Peter; Giegerich, Robert
Title: pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows Document date: 2007_5_3
ID: zgv4kd6j_2
Snippet: Standard RNA folding programs (5,6) neglect pseudoknots for reasons of efficiency. While the standard methods need time proportional to the cube of the input sequence length, pseudoknot prediction is much more demanding. This issue has attracted a large body of bio-informatics work, where all approaches either abandon the model of free energy minimization, or make restrictions on the class of pseudoknots that can be recognized. The well-known alg.....
Document: Standard RNA folding programs (5,6) neglect pseudoknots for reasons of efficiency. While the standard methods need time proportional to the cube of the input sequence length, pseudoknot prediction is much more demanding. This issue has attracted a large body of bio-informatics work, where all approaches either abandon the model of free energy minimization, or make restrictions on the class of pseudoknots that can be recognized. The well-known algorithm by Rivas and Eddy (7) , which is able to predict a restricted class of pseudoknots, needs O(n 6 ) time and O(n 4 ) memory space, where n is the sequence length. Even more restrictive, but more efficient by two orders of magnitude is the program pknotsRG by Reeder and Giegerich (8) , requiring O(n 4 ) time and O(n 2 ) space. The new method presented here re-implements and extends this approach in several significant ways.
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