Depth annotation of RNA folds for secondary structure motif search

Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05

Volumn 2005, Issue , 2005, Pages

  Ashlock, Daniel ^a   Schonfeld, Justin ^b  

^a UNIVERSITY OF GUELPH   (Canada)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; DYNAMIC PROGRAMMING; EVOLUTIONARY ALGORITHMS; MAPPING;

BIOLOGICAL ACTIVITY; EUCLIDEAN PLANES; IRON RESPONSE ELEMENT;

RNA;

EID: 33847217612     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/cibcb.2005.1594896     Document Type: Conference Paper

References (19)

1. Dan Ashlock and Justin Schonfeld. Nonlinear projection for the display of high dimensional distance data. Accepted to CEC 2005, 2005.
2. G. B. Fogel, V. W. Porto, D. G. Weekes, D. B. Fogel, R. H. Griffey, J. A. McNeil, E. Lesnik, D. J. Ecker, and R Sampath. Discovery of ma structural elements using evolutionary computation. Nucleic Acids Research, 30(23):5310-5317, 2002.
3. J. Gorodkin, L. J. Heyer, and G. D. Stormo. Finding the most signi cant common sequence and structure motifs in a set of rna sequences. Nucleic Acids Research, 25(18):3724-3732, 1997.
4. J. Gorodkin, S. L. Stricklin, and G. D. Stormo. Discovering common stem-loop motifs in unaligned rna sequences. Nucleic Acids Research, 29(10):2135-2144, 2001.
5. Daniel Gus eld. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, Boston, 1997.
6. B. R. Henderson, E. Menotti, C. Bonnard, and L. C. Kuhn. Optimal sequence and structure of iron-responsive elements. Journal of Biological Chemistry, 269(26):17481-17489, 1994.
7. M. W. Hentze and L. C. Kuhn. Molecular control of vertebrate iron metabolism:mrna-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. Proc. Natl. Acad. Sci. USA, 93:8175-8182, 1996.
8. Y. Hu. Prediction of consensus structural motifs in a family of coregulated rna sequences. Nucleic Acids Research, 30(17), 2002.
9. Y. Hu. Gprm: a genetic programming approach to nding common rna secondary structure elements. Nucleic Acids Research, 31(13):3446-3449, 2003.
10. Nam J.W., Joung J.G., Ahn Y.S., and Zhang B.T. Two-step genetic programming for optimization of rna common-structure. Applications of Evolutionary Computing Lecture Notes in Computer Science 3005, pages 73-83, 2004.
11. T. Macke, D. Ecker, R. Gutell, D. Gautheret, D.A. Case, and R. Sampath. Rnamotif - a new ma secondary structure de nition and discovery algorithm. Nucleic Acids Research, 29:4724-4735, 2001.
12. D. H. Mathews and D. H. Turner. Dynalign: An algorithm for nding the secondary structure common to two ma sequences. Journal of Molecular Biology, 317:191-203, 2002.
13. D.H. Mathews and M.abd D. H.Zuker J. Sabina. Turner expanded sequence dependence of thermodynamic parameters provides robust prediction of rna secondary structure. Journal of Molecular Biology, 288:910-940, 1999.
14. G. Mauri and G. Pavesi. Pattern discovery in rna secondary structure using af x trees. CPM 2003, LNCS 2676, pages 278-294, 2003.
15. G. Mauri and G. Pavesi. Algorithms for pattern matching and discovery in rna secondary sturcture. Theoretical Computer Science, 335:29-51, 2005.
16. Joao Meidanis and Joao C. Setabal. Introduction to Computational Molecular Biology. Brooks-Cole, Paci c Grove, CA, 1997.
17. Cornelis W. A. Pleij. Rna pseudoknots. Current Opinion in Structural Biology, 4:337-344, 1994.
18. Gilbert Syswerda. A study of reproduction in generational and steady state genetic algorithms. In Foundations of Genetic Algorithms, pages 94-101. Morgan Kaufmann, 1991.
19. M. Zuker, D.H. Mathews, and D.H. Turner. Algorithms and thermo-dynamics for ma secondary structure prediction: A practical guide. In J. Barciszewski and B.F.C. Clark, editors, RNA Biochemistry and Biotechnology. Kluwer Academic Publishers, 1999.