Nanotechnology: Science and Computation pp 121-135 | Cite as

# Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set

## 5 Conclusions

We presented here an algorithm that, given a combinatorial set and parameter *k*, predicts the *k* secondary structures with lowest minimum free energies in the combinatorial set. When the number of words in each set of the overall input-set is considered to be a constant, our algorithm runs in *O*(*skn*^{3}) time. In our algorithms, given a combination *C*, we look at the minimum free energy structure only. Extensions of these problems would be to find suboptimal structures (i.e. whose free energy is greater than the MFE), or to consider pseudoknots. Another problem for future work would be to find an algorithm with better running time, for example *O*(*n*^{3} + *k*).

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## References

- 1.M. Andronescu,
*Algorithms for predicting the secondary structure of pairs and combinatorial sets of nucleic acid strands*, M.Sc. Thesis, U. British Columbia, November 2004. http://www.cs.ubc.ca/grads/resources/thesis/Nov03/Mirela_Andronescu.pdfGoogle Scholar - 2.M. Andronescu, D. Dees, L. Slaybaugh, Y. Zhao, B. Cohen, A. Condon, and S. Skiena, Algorithms for testing that sets of DNA words concatenate without secondary structure,
*DNA-Based Computers*, M. Hagiya, A. Ohuchi, eds., Lecture Notes in Computer Science 2568, Springer (2003) 182–195. (Revised version appeared in Natural Computing, 2(4):391–415, 2003.)Google Scholar - 3.J.V. Ponomarenko, G.V. Orlova, A.S. Frolov, M.S. Gelfand and M.P. Ponomarenko, SELEX DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data,
*Nucl. Acids. Res.*(2002) 30(1): 195–199.CrossRefGoogle Scholar - 4.M. Zuker and P. Stiegler, Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information,
*Nucl. Acids. Res.*(1981) 9: 133–148.Google Scholar