A graphical programming system for molecular motif search

Proceedings of the 5th International Conference on Generative Programming and Component Engineering, GPCE'06

Volumn , Issue , 2006, Pages 131-140

  Reeder, Janina ^a   Giegerich, Robert ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

Dynamic programming; RNA structure

Indexed keywords

COMPUTER ARCHITECTURE; DYNAMIC PROGRAMMING; MOLECULAR STRUCTURE; RNA; SERVERS; XML;

BIOSEQUENCE ANALYSIS.; GRAPHICAL PROGRAMMING SYSTEMS; RNA STRUCTURE; SERVER ARCHITECTURE;

GRAPHICAL USER INTERFACES;

EID: 34547426364     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1173706.1173727     Document Type: Conference Paper

References (18)

1. A. F. Bompfünewerer, C. Flamm, C. Fried, G. Fritzsch, I. L. Hofacker, J. Lehmann, K. Missal, A. Mosig, B. Müller, S. J. Prohaska, B. M. R. Stadler, P. F. Stadler, A. Tanzer, S. Washietl, and C. Witwer. Evolutionary patterns of non-coding rnas. Th. Biosci., 123:301-369, 2005.
2. R. Giegerich, C. Meyer, and P. Steffen. Towards a discipline of dynamic programming. In S. Schubert, B. Reusch, and N. Jesse, editors, Informatik bewegt, GI-Edition - Lecture Notes in Informatics, pages 3-44. Bonner Köllen Verlag, 2002.
3. R. Giegerich, C. Meyer, and P. Steffen. A discipline of dynamic programming over sequence data. Science of Computer Programming, 51(3):215-263, 2004.
4. R. Giegerich and P. Steffen. Challenges in the compilation of a domain specific language for dynamic programming. In Proceedings of the 2006 ACM Symposium on Applied Computing, 2006.
5. R. Giegerich, B. Voss, and M. Rehmsmeier. Abstract Shapes of RNA. Nucleic Acids Res., 32(16):4843-4851, 2004.
6. S. Gräf, G. Steger, D. Strothmann, and S. Kurtz. HyPaLib: a Database of RNAs and RNA Structural Elements defined by Hybrid Patterns. Nucleic Acids Res., 29(1):196-198, 2001.
7. M. W. Hentze and L. C. Kühn. Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. PNAS, 93(16):8175-818, 1996.
8. I. L. Hofacker, W. Fontana, P. F. Stadler, S. Bonhoeffer, M. Tacker, and P. Schuster. Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie, 125:167-188, 1994.
9. G. Hutton. Higher order functions for parsing. Journal of Functional Programming, 3(2):323-343, 1992.
10. Z. Kikinis, R. S. Eisenstein, A. J. E. Bettany, and H. N. Munro. Role of RNA secondary structure of the iron-responsive element in translational regulation of ferritin synthesis. Nucl. Acids Res., 23(20):4190-4195, 1995.
11. T. J. Macke, D. J. Ecker, R. R. Gutell, D. Gautheret, D. A. Case, and R. Sampath. RNAMotif, an RNA secondary structure definition and search algorithm. Nucl. Acids Res., 29(22):4724-4735, 2001.
12. J. S. Mattick. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays, 25(10):930-939, 2003.
13. L. Pachter and B. Sturmfels, editors. Algebraic Statistics for Computational Biology. Cambridge University Press, August 2005.
14. J. Reeder and R. Giegerich. Design, implementation and evaluation of a practical pseudoknot folding algorithm, based on thermodynamics. BMC Bioinformatics, 5:104, 2004.
15. M. Rehmsmeier, P. Steffen, M. Höchsmann, and R. Giegerich. Fast and effective prediction of microRNA/target duplexes. RNA, 10:1507-1517, 2004.
16. G. Rote. Path problems in graphs. Computing Supplements, 7:155-189, 1990.
17. P. Steffen and R. Giegerich. Table design in dynamic programming. Information and Computation, 2006. to appear.
18. M. Zuker and P. Stiegler. Optimal Computer Folding of Large RNA Sequences using Thermodynamics and Auxiliary Information. Nucleic Acids Res., 9:133-148, 1981.