2 1/2 -approximation algorithm for shortest superstring

SIAM Journal on Computing

Volumn 29, Issue 3, 1999, Pages 954-986

  Sweedyk, Z ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; APPROXIMATION THEORY; COMPUTATIONAL COMPLEXITY; DATA COMPRESSION; DNA SEQUENCES; GRAPH THEORY; HEURISTIC METHODS;

SHORTEST SUPERSTRING; SHOTGUN SEQUENCING;

SET THEORY;

EID: 0033293711     PISSN: 00975397     EISSN: None     Source Type: Journal    
DOI: 10.1137/s0097539796324661     Document Type: Article

References (13)

1. C. ARMEN AND C. STEIN, Improved length bounds for the shortest superstring problem, in Proceedings 5th International Workshop on Algorithms and Data Structures, Lecture Notes in Comput. Sci. 955, Springer-Verlag, Berlin, 1995, pp. 494-505.
2. C. ARMEN AND C. STEIN, A 22/3 approximation algorithm for the shortest superstring problem, in Proceedings Combinatorial Pattern Matching, Lecture Notes in Comput. Sci. 1075, Springer-Verlag, Berlin, 1996, pp. 87-101.
3. A. BLUM, T. JIANG, M. LI, J. TROMP, AND M. YANNAKAKIS, Linear approximation of shortest superstrings, in Proceedings 23rd Annual ACM Symposium on Theory of Computing, ACM, New York, 1991, pp. 328-336.
4. D. BRESLAUER, T. JIANG, AND Z. JIANG, Rotations of periodic strings and short superstrings, J. Algorithms, 24 (1997), pp. 340-353.
5. A. CZUMAJ, L. GASIENIEC, M. PIOTROW, AND W. RYTTER, Parallel and sequential approximations of shortest superstrings, in Proceedings First Scandinavian Workshop on Algorithm Theory, Lecture Notes in Comput. Sci. 824, Springer-Verlag, Berlin, 1994, pp. 95-106.
6. T. R. GINGERAS, J. P. MILAO, P. SCIAKY, AND R. J. ROBERTS, Computer programs for the assembly of dna sequences, Nucleic Acid Res., 7 (1979), pp. 529-545.
7. R. KOSARAJU, J. PARK, AND C. STEIN, Long tours and short superstrings, in Proc. 35th Annual IEEE Symposium on Foundations of Computer Science, IEEE Computer Society Press, Piscataway, NJ, 1994, pp. 166-177.
8. A. LESK, ED., Computational Molecular Biology, Sources and Methods for Sequence Analysis, Oxford University Press, Oxford, 1988.
9. J. STORER, Data Compression: Methods and Theory, Computer Science Press, Rockville, MD, 1988.
10. E. SWEEDYK, A 21/2 Approximation Algorithm for Shortest Common Superstring, Ph.D. Thesis, University of California at Berkeley, Berkeley, CA, 1995.
11. S. TENG AND F. YAO, Approximating shortest superstrings, in Proc. 34th Annual IEEE Symposium on Foundations of Computer Science, IEEE Computer Society Press, Los Alamitos, CA, 1993, pp. 158-165.
12. J. TURNER, Approximation algorithms for the shortest common superstring problem, Inform. and Comput., 83 (1989), pp. 1-20.
13. E. UKKONEN, On-line Construction of Suffix-Trees, Technical Report A-1993, Department of Computer Science, University of Helsinki, Finland, 1993.