Implementing algebraic dynamic programming in the functional and the imperative programming paradigm

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 2386, Issue , 2002, Pages 1-20

  Giegerich, Robert ^a   Steffen, Peter ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGEBRA; ALGORITHMS; COMPUTATIONAL LINGUISTICS; FUNCTIONAL PROGRAMMING; SPECIFICATION LANGUAGES; SPECIFICATIONS; TRANSLATION (LANGUAGES);

ABSTRACT SPECIFICATIONS; ALGEBRAIC DYNAMIC PROGRAMMING; ASYMPTOTIC EFFICIENCY; DYNAMIC PROGRAMMING ALGORITHM; IMPERATIVE LANGUAGES; IMPERATIVE PROGRAMMING; LAZY FUNCTIONAL LANGUAGES; SOURCE-TO-SOURCE TRANSFORMATIONS;

DYNAMIC PROGRAMMING;

EID: 84959041656     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-45442-X_1     Document Type: Conference Paper

References (21)

1. A.V. Aho and J.D. Ullman. The Theory of Parsing, Translation and Compiling. Prentice-Hall, Englewood Cliffs, NJ, 1973. I and II.
2. R. Bellman. Dynamic Programming. Princeton University Press, 1957.
3. W.S. Brainerd. Tree generating regular systems. Information and Control, 14:217–231, 1969.
4. R. Durbin, S. Eddy, A. Krogh, and G. Mitchison. Biological Sequence Analysis. Cambridge University Press, 1998.
5. D. Evers and R. Giegerich. Reducing the conformation space in RNA structure prediction. In German Conference on Bioinformatics, pages 118–124, 2001.
6. R. Giegerich. A systematic approach to dynamic programming in bioinformatics. Bioinformatics, 16:665–677, 2000.
7. R. Giegerich, S. Kurtz, and G. F. Weiller. An algebraic dynamic programming approach to the analysis of recombinant DNA sequences. In Proc. of the First Workshop on Algorithmic Aspects of Advanced Programming Languages, pages 77–88, 1999.
8. R. Giegerich and C. Meyer. Algebraic dynamic programming. In Proc. of the 9th International Conference on Algebraic Methodology And Software Technology, 2002. To appear.
9. R. Giegerich and K. Schmal. Code selection techniques: Pattern matching, tree parsing and inversion of derivors. In Proc. European Symposium on Programming 1988, Lecture Notes in Computer Science 300, Springer Verlag, pages 247–268, 1988.
10. S.L. Graham and M.A. Harrison. An improved context-free recognizer. ACM Transactions on Programming Languages and Systems, 2(3):415–462, 1980.
11. D. Gusfield. Algorithms on Strings, Trees, and Sequences. Computer Science and Computational Biology. Cambridge University Press, 1997.
12. M. Höchsmann. Tree and Forest Alignments - An Algebraic Dynamic Programming Approach for Aligning Trees and Forests. Master’s thesis, Bielefeld University, Mai 2001.
13. G. Hutton. Higher order functions for parsing. Journal of Functional Programming, 3(2):323–343, 1992.
14. C. Meyer and R. Giegerich. Matching and Significance Evaluation of Combined Sequence-Structure Motifs in RNA. Z.Phys.Chem., 216:193–216, 2002.
15. T.L. Morin. Monotonicity and the principle of optimality. Journal of Mathematical Analysis and Applications, 86:665–674, 1982.
16. E. Rivas and S. Eddy. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol., 285:2053–2068, 1999.
17. D.B. Searls. Linguistic approaches to biological sequences. CABIOS, 13(4):333–344, 1997.
18. K. Sikkel and M. Lankhorst. A parallel bottom-up tomita parser. In G. Görz, editor, 1. Konferenz Verarbeitung natürlicher Sprache (KONVENS’92), Nürnberg, Germany, Informatik Aktuell, pages 238–247. Springer-Verlag, 1992.
19. P. Steffen. Basisfunktionen für die Übersetzung von Programmen der Algebraischen Dynamischen Programmierung. Master’s thesis, Bielefeld University, February 2002. In German.
20. M. Tomita. Efficient Parsing for Natural Language — A Fast Algorithm for Practical Systems. Int. Series in Engineering and Computer Science. Kluwer, Hingham, MA, 1986.
21. M. Zuker and S. Sankoff. RNA secondary structures and their prediction. Bull. Math. Biol., 46:591–621, 1984.