On average sequence complexity

Theoretical Computer Science

Volumn 326, Issue 1-3, 2004, Pages 213-227

  Janson, Svante ^a   Lonardi, Stefano ^b   Szpankowski, Wojciech ^c  

^a UPPSALA UNIVERSITY   (Sweden)

^b University of California Riverside   (United States)

^c Purdue University   (United States)

Author keywords

Complexity index; Sequence subword complexity; Suffix tree

Indexed keywords

ASYMPTOTIC STABILITY; DATA COMPRESSION; DNA; FUNCTIONS; GENES; MATHEMATICAL MODELS; PROBABILITY; PROTEINS; RANDOM PROCESSES; STATISTICAL METHODS;

COMPLEXITY INDEX; LEMPEL-ZIV COMPLEXITY; PROKARYOTIC GENOMES; SEQUENCE/SUBWORD COMPLEXITY; SUFFIX TREE;

COMPUTATIONAL COMPLEXITY;

EID: 5144221374     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2004.06.023     Document Type: Article

References (29)

1. A. Apostolico, M.E. Bock, S. Lonardi, Monotony of surprise and large-scale quest for unusual words, J. Comput. Biol. 10 (3-4) (2003) 283-311.
2. A. Apostolico, M.E. Bock, S. Lonardi, X. Xu, Efficient detection of unusual words, J. Comput. Biol. 7 (1/2) (2000)71-94.
3. A. Apostolico, W. Szpankowski, Self-alignment in words and their applications, J. Algorithms 13 (3) (1992) 446-467.
4. A.D. Barbour, L. Holst, S. Janson, Poisson Approximation, Oxford Press, Oxford, 1992.
5. T.C. Bell, J.G. Cleary, I.H. Witten, Text Compression, Prentice-Hall, Englewood Cliffs, NJ, 1990.
6. C. Burge, A. Campbell, S. Karlin, Over- and under-representation of short oligonucleotides in DNA sequences, Proc. Natl. Acad. Sci. USA. 89 (1992) 1358-1362.
7. W.I. Chang, E.L. Lawler, Sublinear approximate string matching and biological applications, Algorithmica 12 (4/5) (1994) 327-344.
8. M.T. Chen, J. Seiferas, Efficient and elegant subword tree construction, in: A. Apostolico, Z. Galil (Eds.), Combinatorial Algorithms on Words, NATO Advanced Science Institutes, Series F, Vol. 12, Springer, Berlin, 1985, pp. 97-107.
9. A. De Luca, On the combinatorics of finite words, Theoret. Comput. Sci. 218 (1) (1999) 13-39.
10. M. Farach, Optimal suffix tree construction with large alphabets, in: Proc. 38th Annual Symp. on Foundations of Computer Science, 1997, pp. 137-143.
11. J.W. Fickett, D.C. Torney, D.R. Wolf, Base compositional structure of genomes, Genomics 13 (1992) 1056-1064.
12. A. Flaxman, A.W. Harrow, G.B. Sorkin, Strings with maximally many distinct subsequences and substrings, Electron. J. Combin. 11 1 (2004).
13. L. Ilie, S. Yu, K. Zhang, Repetition complexity of words, in: Proc. Internat. Computing and Combinatorics Conference 2002, pp. 320-329.
14. S. Karlin, C. Burge, A.M. Campbell, Statistical analyses of counts and distributions of restriction sites in DNA sequences, Nucleic Acids Res. 20 (1992) 1363-1370.
15. S. Karlin, J. Mrazek, A.M. Campbell, Frequent oligonucleotides and peptides of the Haemophilus influenzae genome, Nucleic Acids Res. 24 (21) (1996) 4273-4281.
16. Z. Kása, On the d-complexity of strings, Pure Math. Appl. 9 (1-2) (1998) 119-128.
17. F. Leve, P. Séébold, Proof of a conjecture on word complexity, Bull. Belg. Math. Soc. 8(2) (2001).
18. M. Li, P. Vitanyi, Introduction to Kolmogorov Complexity and its Applications, Springer, Berlin, August 1993.
19. M. Lothaire (Ed.), Algebraic Combinatorics on Words, Cambridge University Press, Cambridge, 2002.
20. E.M. McCreight, A space-economical suffix tree construction algorithm, J. Assoc. Comput. Mach. 23 (2) (1976) 262-272.
21. H. Niederreiter, Some computable complexity measures for binary sequences, in: C. Ding, T. Hellseth, H. Niederreiter (Eds.), Sequences and Their Applications, Springer, Berlin, 1999, pp. 67-78.
22. P.A. Pevzner, M.Y. Borodovsky, A.A. Mironov, Linguistics of nucleotides sequences II: stationary words in genetic texts and the zonal structure of DNA, J. Biomol. Struct. Dynamics 6 (1989) 1027-1038.
23. G. Reinert, S. Schbath, M.S. Waterman, Probabilistic and statistical properties of words: an overview, J. Comput. Biol. 7 (2000) 1-46.
24. J. Shallit, On the maximum number of distinct factors in a binary string, Graphs Combin. 9 (1993) 197-200.
25. W. Szpankowski, A generalized suffix tree and its (un)expected asymptotic behaviors, SIAM J. Comput. 22 (1993) 1176-1198.
26. W. Szpankowski, Average Case Analysis of Algorithms on Sequences, Wiley, New York, 2001.
27. O.G. Troyanskaya, O. Arbell, Y. Koren, G.M. Landau, A. Bolshoy, Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity, Bioinformatics 18 (5) (2002) 679-688.
28. E. Ukkonen, On-line construction of suffix trees, Algorithmica 14 (3) (1995) 249-260.
29. P. Weiner, Linear pattern matching algorithm, in: Proc. 14th Annual IEEE Symp. on Switching and Automata Theory, Washington, DC, 1973, pp. 1-11.