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

@article{Ogurtsov2006AnalysisOI,
  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},
  journal={Bioinformatics},
  year={2006},
  volume={22 11},
  pages={1317-24}
}
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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References

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Showing 1-10 of 28 references

Mfold web server for nucleic acid folding and hybridization prediction

Nucleic Acids Research • 2003
View 4 Excerpts
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The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides

R. Kretschmer-Kazemi Far, G. Sczakiel
Nucleic Acids Res., • 2003

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Bohula, E.A
J Biol Chem., • 2003

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