Searching for supermaximal repeats in large DNA sequences

Communications in Computer and Information Science

Volumn 13, Issue , 2008, Pages 87-101

  Lian, Chen Na ^a   Halachev, Mihail ^a   Shiri, Nematollaah ^a  

^a Dept of Electrical and Computer Engineering   (Canada)

Author keywords

DNA sequences; Performance; Suffix tree; Supermaximal repeats

Indexed keywords

BIOINFORMATICS; BIRDS; CHROMOSOMES; DNA; FORESTRY; TREES (MATHEMATICS);

HUMAN CHROMOSOMES; INDEX STRUCTURE; PERFORMANCE; SPACE REQUIREMENTS; SUFFIX-TREES; SUPERMAXIMAL REPEATS;

DNA SEQUENCES;

EID: 84885756680     PISSN: 18650929     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-540-70600-7_7     Document Type: Article

References (18)

1. Halachev, M., Shiri, N., Thamildurai, A.: Efficient and scalable indexing techniques for biological sequence data. In: Hochreiter, S., Wagner, R. (eds.) BIRD 2007. LNCS (LNBI), vol. 4414, pp. 464-479. Springer, Heidelberg (2007)
2. Vmatch: large scale sequence analysis software, http://www.vmtach.de
3. Gusfield, D.: Algorithms on strings, trees and sequences: computer science and computational biology. Cambridge University Press, New York (1997)
4. Korf, B.R.: Human Genetics: A Problem-Based Approach. Blackwell, Boston (2000)
5. Watson, J., Hopkins, N., Roberts, J., Steitz, J., Weiner, A.: Molecular Biology of the Gene, 6th edn. Benjamin-Cummings, Menlo Park (2007)
6. Kurtz, S.: Reducing the space requirement of suffix trees. Software Practice and Experience 29(13), 1149-1171 (1999)
7. Grossi, R., Vitter, J.S.: Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching. SIAM Journal on Computing 35(2), 378-407 (2005)
8. Ferragina, P., Manzini, G.: Opportunistic data structures with applications. In: 41st IEEE Symposium on Foundations of Computer Science, pp. 390-398 (2000)
9. Valimaki, N., Gerlach, W., Dixit, K., Makinen, V.: Compressed suffix tree-a basis for genome-scale sequence analysis. Bioinformatics 23(5), 629-630 (2007)
10. Hon, W.-K., Lam, T.W., Sung, W.-K., Tse, W.-L., Wong, C.-K., Yiu, S.-M.: Practical Aspects of Compressed Suffix Arrays and FM-index in Searching DNA Sequences. In: 6th Workshop on Algorithm Engineering and Experiments, pp. 31-38 (2004)
11. Kurtz, S., Schleiermacher, C.: REPuter: Fast Computation of Maximal Repeats in Complete Genomes. Bioinformatics 15, 426-427 (1999)
12. RepeatMatch, http://mummer.sourceforge.net/manual/#repeat
13. RepeatMasker, http://repeatmasker.org/
14. Bedell, J.A., Korf, I., Gish, W.: MaskerAid: a Performance Enhancement to Repeat-Masker. Bioinformatics 16(11), 1040-1041 (2000)
15. Gotoh, O.: An Improved Algorithm for Matching Biological Sequences. Journal of Molecular Biology 162(3), 705-708 (1982)
16. Abouelhoda, M.I., Kurtz, S., Ohlebusch, E.: Replacing suffix tree with enhances suffix arrays. Journal of Discrete Algorithms 2(1), 53-86 (2004)
17. Miki, B.L., Neelin, J.M.: DNA repeat lengths of erythrocyte chromatins differing in content of histones H1 and H5. Nucleic Acids Res. 8(3), 529-542 (1980)
18. National Center for Biotechnology Information, http://www.ncbi.nim.nih.gov