Locating maximal multirepeats in multiple strings under various constraints

Computer Journal

Volumn 50, Issue 2, 2007, Pages 178-185

  Bakalis, A ^a   Iliopoulos, C S ^a   Makris, C ^b   Sioutas, S ^b   Theodoridis, E ^b   Tsakalidis, A ^b   Tsichlas, K ^b  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF PATRAS   (Greece)

Author keywords

Computational biology; Maximal repeats; Search trees; Suffix trees; Tandem arrays

Indexed keywords

ALGORITHMS; BIOLOGY; COMPUTER SIMULATION;

COMPUTATIONAL BIOLOGY; MULTIPLE STRINGS; MULTIREPEATS;

COMPUTATION THEORY;

EID: 33947269364     PISSN: 00104620     EISSN: 14602067     Source Type: Journal    
DOI: 10.1093/comjnl/bxl058     Document Type: Article

References (16)

1. Crochemore, M. (1981) An optimal algorithm for computing the repetitions in a word. Inform. Process. Lett., 12, 244-249.
2. Main, M.G. and Lorentz, R.J. (1984) An O(n log n) algorithm for finding all repetitions in a string. J. Algorithm., 5, 422-432.
3. Kolpakov, R.M. and Kucherov, G. (1999) Finding maximal repetitions in a word in linear time. Proceedings of FOCS 99, New York City, DC., NY, October 17-19, pp. 596-604, IEEE Computer Society, Washington, DC.
4. Gusfield, D. and Stoye, J. (2004) Linear time algorithms for finding and representing all the tandem repeats in a string. J. Comput. Sys. Sci., 69, 525-546.
5. Landau, G.M., Schmidt, J.P. and Sokol, D. (2001) An algorithm for approximate tandem repeats. J. Comput. Biol., 8, 1-18.
6. Kolpakov, R.M. and Kucherov, G. (2003) Finding approximate repetitions under Hamming distance. Theor. Comput. Sci., 303, 135-156.
7. Benson, G. (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
8. Groult, R., Leonard, M. and Mouchard, L. (2004) Speeding up the detection of evolutive tandem repeats. Theor. Comput. Sci., 310, 309-328.
9. Wexler, Y., Yakhini, Z., Kashi, Y. and Geiger, D. (2005) Finding approximate tandem repeats in genomic sequences. J. Comput. Biol., 12, 928-942.
10. Crochemore, M. and Sagot, M.-F. (2004) Motifs in sequences: Localization and extraction. In Crabbe, J., Drew, M. and Konopka, A. (eds), Handbook of Computational Chemistry, Marcel Dekker Inc., New York.
11. Marsan, L. and Sagot, M.-F. (2000) Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J. Comput. Biol., 7, 345-360.
12. Gusfield, D. (1997) Algorithms on Strings, Trees, and Sequences. Cambridge University Press, New York.
13. Brodal, G.S., Lyngs, R.B., Pedersen, C.N.S. and Stoye, J. (1999), Finding maximal pairs with bounded gaps. Proceedings of CPM 99, Warwick University, UK, July 22-24, pp. 134-149. Springer-Verlag, Berlin.
14. Kurtz, S., Choudhuri, J.V., Ohlebusch, E., Schleiermacher, C., Stoye, J. and Giegerich, R. (2001) REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res., 29, 4633-4642.
15. Adel'son-Vel'skii, G.M. and Landis, Y.M. (1962) An algorithm for the organization of Information. Doklady Akademii Nauk SSSR, 146, 263-266. English translation in Soviet Math. Dokl., 3, 1259-1262.
16. Brown, M.R. and Tarjan, R.E. (1980) Design and analysis of a data structure for representing sorted lists. SIAM J. Comput., 9, 594-614.