Analysis of internal loops within the RNA secondary structure in almost quadratic time

  title={Analysis of internal loops within the RNA secondary structure in almost quadratic time},
  author={Aleksey Y. Ogurtsov and Svetlana A. Shabalina and Alexey S. Kondrashov and Mikhail A. Roytberg},
  volume={22 11},
MOTIVATION Evaluating all possible internal loops is one of the key steps in predicting the optimal secondary structure of an RNA molecule. The best algorithm available runs in time O(L(3)), L is the length of the RNA. RESULTS We propose a new algorithm for evaluating internal loops, its run-time is O(M(*)log(2)L), M < L(2) is a number of possible nucleotide pairings. We created a software tool Afold which predicts the optimal secondary structure of RNA molecules of lengths up to 28 000 nt… CONTINUE READING
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