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Problems on RNA Secondary Structure Prediction and Design

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Automata, Languages and Programming (ICALP 2003)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2719))

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Abstract

We describe several computational problems on prediction and design of RNA molecules.

This material is based upon work supported by the U.S. National Science Foundation under Grant No. 0130108, by the National Sciences and the Engineering Research Council of Canada, and by the by the Defense Advanced Research Projects Agency (DARPA) and Air Force Research Laboratory, Air Force Materiel Command, USAF, under agreement number F30602-01-2-0555.

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References

  1. T. Akutsu, “Dynamic programming algorithms for RNA secondary prediction with pseudoknots”, Discrete Applied Mathematics, 104, 2000, 45–62.

    Article  MATH  MathSciNet  Google Scholar 

  2. M. Andronescu, R. Aquirrez-Hernandez, H. Hoos, and A. Condon, “RNAsoft: a suite of RNA secondary structure prediction and design software tools”, Nucleic Acids Research, In press.

    Google Scholar 

  3. M. Andronescu,, D. Dees, L. Slaybaugh, Y. Zhao, A. Condon, B. Cohen, and S. Skiena, “Algorithms for testing that sets of DNA words concatenate without secondary structure”, Proc. Eighth International Workshop on DNA Based Computers, Hokkaido, Japan, June 2002. To appear in LNCS.

    Google Scholar 

  4. L.M. Adleman, “Molecular computation of solutions to combinatorial problems,” Science, Vol 266, 1994, 1021–1024.

    Article  Google Scholar 

  5. A. Ben-Dor, R. Karp, B. Schwikowski, and Z. Yakhini, “Universal DNA tag systems: a combinatorial design scheme,” Proc. Fourth Annual International Conference on Computational Molecular Biology (RECOMB) 2000, ACM, 65–75.

    Google Scholar 

  6. Braich, R. S., Chelyapov, N., Johnson, C., Rothemund, P. W.K. and Adleman, L. “Solution of a 20-variable 3-SAT Problem on a DNA computer”, Science 296, 2002, 499–502.

    Article  Google Scholar 

  7. S. Brenner, M. Johnson, J. Bridgham, G. Golda, D.H. Lloyd, D. Johnson, S. Luo, S. McCurdy, M. Foy, M, Ewan, R. Roth, D. George, S. Eletr, G. Albrecht, E. Vermaas, S.R. Williams, K. Moon, T. Burcham, M. Pallas, R.B. DuBridge, J. Kirchner, K. Fearon, J. Mao, and K. Corcoran, “Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays,” Nature Biotechnology, 18, 2000, 630–634.

    Article  Google Scholar 

  8. S. Brenner, “Methods for sorting polynucleotides using oligonucleotide tags,” U.S. Patent Number 5,604,097, 1997.

    Google Scholar 

  9. C. Dennis, “The brave new world of RNA”, Nature, 418,11 2002, 122–124.

    Article  Google Scholar 

  10. R. G. Downey and M. R. Fellows, “Fixed-Parameter Tractability and Completeness I: Basic Results”, SIAM J. Comput. 24(4), 1995, 873–921.

    Article  MATH  MathSciNet  Google Scholar 

  11. D. Faulhammer, A.R. Cukras, R.J. Lipton, and L. F. Landweber, “Molecular computation: RNA solutions to chess problems,” Proc. Natl. Acad. Sci. USA, 97, 2000, 1385–1389.

    Article  Google Scholar 

  12. .P. Gultyaev, F.H.D. van Batenburg, and C.W.A. Pleij, “The computer simulation of RNA folding pathways using a genetic algorithm”, J. Mol. Biol., 250, 1995, 37–51.

    Article  Google Scholar 

  13. I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, and P. Schuster, “Fast Folding and Comparison of RNA Secondary Structures”, Monatsh.Chem. 125, 1994, 167–188.

    Article  Google Scholar 

  14. M. Jerrum and A. Sinclair, “Approximating the permanent”, SIAM Journal on Computing 18, 1989, 1149–1178.

    Article  MATH  MathSciNet  Google Scholar 

  15. R.B. Lyngsø and C.N.S. Pedersen, “Pseudoknot prediction in energy based models”, Journal of Computational Biology 7(3), 2000, 409–427.

    Article  Google Scholar 

  16. R. B. Lyngso, M. Zuker, and C. N. S. Pedersen, “Internal Loops in RNA Secondary Structure Prediction”, Proc. Third International Conference in Computational Molecular Biology (RECOMB), April 1999, 260–267.

    Google Scholar 

  17. D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner, “Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure”, J. Molecular Biology, 288, 1999, 911–940.

    Article  Google Scholar 

  18. J.S. McCaskill, “The equilibrium partition function and base pair binding probabilities for RNA secondary structure,” Biopolymers, 29, 1990, 1105–1119.

    Article  Google Scholar 

  19. E. Rivas and S. Eddy, “A dynamic programming algorithm for RNA structure prediction including pseudoknots,” Journal of Molecular Biology, 285, 1999, 2053–2068.

    Article  Google Scholar 

  20. P.W.K. Rothemund and E. Winfree, “The program-size complexity of selfassembled squares”, Symposium on Theory of Computing, 2000.

    Google Scholar 

  21. J. SantaLucia, “A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics”, Proc. Natl Acad Sci USA 95:4, 1998, 1460–1465.

    Article  Google Scholar 

  22. N.C. Seeman, “De novo design of sequences for nucleic acid structural engineering,” Journal of Biomolecular Structure and Dynamics, 8:3, 1990, 573–581.

    Google Scholar 

  23. M.J. Serra, D.H. Turner, and S.M. Freier, “Predicting thermodynamic properties of RNA”, Meth. Enzymol., 259, 1995, 243–261.

    Google Scholar 

  24. D. D. Shoemaker, D. A. Lashkari, D. Morris, M. Mittman, and R. W. Davis, “Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy,” Nature Genetics, 16, 1996, 450–456.

    Article  Google Scholar 

  25. B.A. Sullenger and E. Gilboa. “Emerging clinical applications of RNA”, Nature, 418, 2002, 252–258.

    Article  Google Scholar 

  26. J.W. Szostak, D.P. Bartel, and L. Luisi. “Synthesizing life”, Nature 409, 2001, 387–389.

    Article  Google Scholar 

  27. I. Tinoco Jr. and C. Bustamante, “How RNA folds”, J. Mol. Biol. 293, 1999, 271–281.

    Article  Google Scholar 

  28. Y. Uemura, A. Hasegawa, Y. Kobayashi, and T. Yokomori, “Tree adjoining grammars for RNA structure prediction”, Theoretical Computer Science, 210, 1999, 277–303.

    Article  MATH  MathSciNet  Google Scholar 

  29. E. Westhof and V. Fritsch, “RNA folding: beyond Watson-Crick pairs”, Structure 2000, 8:R55–R65, 2000.

    Article  Google Scholar 

  30. E. Winfree, F. Liu, L. Wenzler, and N. Seeman, “Design and self-assembly of 2D DNA crystals,” Nature, 394, 1998, 539–544.

    Article  Google Scholar 

  31. S. Wuchty, W. Fontana, I. L. Hofacker, and P. Schuster, “Complete Suboptimal Folding of RNA and the Stability of Secondary Structures”, Biopolymers, 1998, Vol. 49, 145–165.

    Article  Google Scholar 

  32. M. Zuker and P. Steigler, “Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information,” Nucleic Acids Res 9, 1981, 133–148.

    Article  Google Scholar 

  33. M. Zuker, “On Finding All Suboptimal Foldings of an RNA Molecule”, Science, 244, 1989, 48–52.

    Article  MathSciNet  Google Scholar 

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Author information

Authors and Affiliations

  1. The Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, B.C., V6R2C8

    Anne Condon

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  1. Anne Condon
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Editor information

Editors and Affiliations

  1. Dept. of Mathematics and Computer Science, Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands

    Jos C. M. Baeten

  2. School of Industrial and Systems Engineering, Georgia Institute of Technology, 765 Ferst Drive, Atlanta, GA, 30332-0205, USA

    Jan Karel Lenstra

  3. Department of Information Technology, Uppsala University, P.O. Box 337, 75105, Uppsala, Sweden

    Joachim Parrow

  4. Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands

    Gerhard J. Woeginger

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© 2003 Springer-Verlag Berlin Heidelberg

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Condon, A. (2003). Problems on RNA Secondary Structure Prediction and Design. In: Baeten, J.C.M., Lenstra, J.K., Parrow, J., Woeginger, G.J. (eds) Automata, Languages and Programming. ICALP 2003. Lecture Notes in Computer Science, vol 2719. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45061-0_2

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  • DOI: https://doi.org/10.1007/3-540-45061-0_2

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-40493-4

  • Online ISBN: 978-3-540-45061-0

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