A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays

Bioinformatics

Volumn 25, Issue 13, 2009, Pages 1609-1616

  Khan, Zia ^a,b   Bloom, Joshua S ^b   Kruglyak, Leonid ^b   Singh, Mona ^a,b  

^a Princeton University   (United States)

^b PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER SIMULATION; GENE SEQUENCE; GENETIC ALGORITHM; HUMAN; INFORMATION STORAGE; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE;

ALGORITHMS; BASE SEQUENCE; GENOMICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 67649159244     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp275     Document Type: Article

References (25)

1. Abouelhoda,M.I. et al. (2004) Replacing suffix trees with enhanced suffix arrays. J. Discrete Algorithms, 2, 53-86.
2. Abouelhoda,M.I. et al. (2006) Enhanced suffix arrays and applications. Chapter 7. In Aluru,S. (ed.), Handbook of Computational Molecular Biology. Chapman & Hall/CRC Computer and Information Science Series, Boca Raton, FL, USA, pp. 7-28.
3. Bray,N. and Pachter,L. (2004) MAVID: Constrained ancestral alignment of multiple sequences. Genome Res., 14, 693-699.
4. Choi,J.-H. et al. (2005) GAME: A simple and efficient whole genome alignment method using maximal exact match filtering. Comp. Biol. Chem., 29, 244-253.
5. Drosophila 12 Genomes Consortium. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450, 203-218.
6. Eid,J. et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science, 323, 133-138.
7. Ferragina,P. and Fischer,J. (2007) Suffix arrays on words. In Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM'07). Vol. of Lecture Notes in Computer Science, Springer, Berlin, Germany, pp. 328-339.
8. Ferragina,P. et al. (2009) Compressed text indexes: From theory to practice. ACM J. Exp. Algorithmics (JEA), 13, Article No. 12.
9. Gusfield,D. (1997) Algorithms on Strings, Trees, and Sequences. Cambridge University Press, New York.
10. Höhl,M. et al. (2002) Efficient multiple genome alignment. Bioinformatics, 18 (Suppl 1), S312-S320.
11. Istrail,S. et al. (2004) Whole-genome shotgun assembly and comparison of human genome assemblies. Proc. Natl Acad. Sci. USA, 101, 1916-1921.
12. Kärkkäinen,J. and Ukkonen,E. (1996) Sparse suffix trees. In Cai,J.-Y. and Wong,C.K. (eds), COCOON 1996. Vol. 1090 of Lecture Notes in Computer Science. Springer, Heidelberg, pp. 219-230.
13. Kasai,T. et al. (2001) Linear-time longest-common-prefix computation in suffix arrays and its applications. In Proceedings of the 12th Symposium on Combinatorial Pattern Matching (CPM '01). Vol. 2089 of Lecture Notes in Computer Science. Springer, Berlin, Germany, pp. 181-192.
14. Kurtz,S. (1999) Reducing the space requirement of suffix trees. Soft. Pract. Exp., 29, 1149-1171.
15. Kurtz,S. et al. (2004)Versatile and open software for comparing large genomes. Genome Biol., 5, R12.
16. Larsson,N.J. and Sadakane,K. (2007) Faster suffix sorting. Theor. Comp. Sci., 387, 258-272.
17. Manber,U. and Myers,G.W. (1993) Suffix arrays: A new method for on-line string searches. SIAM J. Comput., 22, 935-948.
18. Manzini,G. (2004) Two space saving tricks for linear time LCP array computation. In Hagerup,T. and Katajainen,J. (eds), SWAT 2004. Vol. 3111 of Lecture Notes in Computer Science. Springer-Verlag, Berlin Heidelberg, pp. 372-383.
19. McIlroy,P.M. et al. (1993) Engineering radix sort. Comput. Syst., 6, 5-27.
20. Myers,E.W. et al. (2000) A whole-genome assembly of Drosophila. Science, 287, 2196-2204.
21. Ohlebusch,E. and Kurtz,S. (2008) Space efficient computation of rare maximal exact matches between multiple sequences. J. Comput. Biol. 15, 357-377.
22. Paux,E. et al. (2008) A physical map of the 1-gigabase bread wheat chromosome 3B. Science, 322, 101-104.
23. Pop,M. and Salzberg,S.L. (2008) Bioinformatics challenges of new sequencing technology. Trends Genet., 24, 142-149.
24. Schatz,M.C. et al. (2007) High-throughput sequence alignment using graphics processing units. BMC Bioinformatics, 8, 474.
25. Schwartz,S. et al. (2003) Human-mouse alignments with BLASTZ. Genome Res., 13, 103-107.