A fast divide-and-conquer algorithm for indexing human genome sequences

IEICE Transactions on Information and Systems

Volumn E94-D, Issue 7, 2011, Pages 1369-1377

  Loh, Woong Kee ^a   Moon, Yang Sae ^b   Lee, Wookey ^c  

^a Sungkyul University   (South Korea)

^b Kangwon National University   (South Korea)

^c Inha University   (South Korea)

Author keywords

Divide and conquer; Human genome sequences; Indexing; Memory bottleneck problem; Parallel processing; Suffix tree

Indexed keywords

FORESTRY; GENES; GENETIC ENGINEERING; INDEXING (OF INFORMATION); PROGRAM PROCESSORS;

DIVIDE AND CONQUER; HUMAN GENOMES; MEMORY BOTTLENECK; PARALLEL PROCESSING; SUFFIX-TREES;

INDEXING (MATERIALS WORKING);

EID: 79959976742     PISSN: 09168532     EISSN: 17451361     Source Type: Journal    
DOI: 10.1587/transinf.E94.D.1369     Document Type: Article

References (24)

1. S. Altschul, T. Madden, A. Schaffer, J. Zhang, W. Miller, and D. Lipman, "Gapped BLAST and PSI-BLAST: A new generation of protein database search programs," Nucleic Acids Research, vol.25, no.17, pp.3389-3402, 1997. (Pubitemid 27359211)
2. M. Atkinson and M. Jordan, "Providing orthogonal persistence for Java," Proc. European Conf. on Object-Oriented Programming (ECOOP), pp.383-395, Brussels, Belgium, July 1998. (Pubitemid 128110400)
3. M. Barsky, U. Stege, A. Thomo, and C. Upton, "A new method for indexing genomes using on-disk suffix trees," Proc. ACM Conference on Information and Knowledge Management (CIKM), pp.649-658, Napa Valley, California, Oct. 2008.
4. S.J. Bedathur and J.R. Haritsa, "Engineering a fast online persistent suffix tree construction," Proc. Int'l Conf. on Data Engineering (ICDE), IEEE, pp.720-731, Boston, Massachusetts, March 2004.
5. C.-F. Cheung, J. Yu, and H. Lu, "Constructing suffix tree for gigabyte sequences with megabyte memory," IEEE Trans. Knowl. Data Eng., vol.17, no.1, pp.90-105, Jan. 2005. (Pubitemid 40536473)
6. P. Ferragina and G. Manzini, "Opportunistic data structures with applications," Proc. Annual Symp. Foundations of Computer Science (FOCS), pp.390-398, Redondo Beach, California, Nov. 2000. (Pubitemid 32075908)
7. A. Ghoting and K. Makarychev, "Serial and parallel methods for i/o efficient suffix tree construction," Proc. Int'l Conf. Management of Data, ACM SIGMOD, pp.827-840, Providence, Rhode Island, June 2009.
8. R. Giegerich, S. Kurtz, and J. Stoye, "Efficient implementation of lazy suffix trees," Software: Practice and Experience (SPE), vol.33, no.11, pp.1035-1049, 2003.
9. D. Gusfield, Algorithms on Strings, Trees, and Sequences, Cambridge University Press, 1997.
10. W.-K. Hon, R. Shah, S.V. Thankachan, and J.S. Vitter, "On entropycompressed text indexing in external memory," Proc. String Processing and Information Retrieval Symposium (SPIRE), pp.75-89, Saariselka, Finland, Aug. 2009.
11. E. Hunt, M.P. Atkinson, and R.W. Irving, "Database indexing for large DNA and protein sequence collections," VLDB Journal, vol.11, no.3, pp.256-271, 2002. (Pubitemid 36156206)
12. S. Kurtz, "Reducing the space requirement of suffix trees," Software: Practice and Experience (SPE), vol.29, no.13, pp.1149-1171, Nov. 1999. (Pubitemid 129303954)
13. S. Kurtz and C. Schleiermacher, "REPuter: Fast computation of maximal repeats in complete genomes," Bioinformatics, vol.15, no.5, pp.426-427, May 1999. (Pubitemid 29312632)
14. B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg, "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome," Genome Biology, vol.10, no.3, pp.R25.1-R25.10, March 2009.
15. H. Li and R. Durbin, "Fast and accurate short read alignment with Burrows-Wheeler transform," Bioinformatics, vol.25, no.14, pp.1754-1760, July 2009.
16. H. Li and R. Durbin, "Fast and accurate long-read alignment with Burrows-Wheeler transform," Bioinformatics, vol.26, no.5, pp.589-595, March 2010.
17. R. Li, C. Yu, Y. Li, T.-W. Lam, S.-M. Yiu, K. Kristiansen, and J. Wang, "SOAP2: An improved ultrafast tool for short read alignment," Bioinformatics, vol.25, no.15, pp.1966-1967, Aug. 2009.
18. B. Phoophakdee and M.J. Zaki, "Genome-scale disk-based suffix tree indexing," Proc. Int'l Conf. on Management of Data, pp.833-844, ACM SIGMOD, Beijing, China, June 2007. (Pubitemid 47630857)
19. B. Phoophakdee and M.J. Zaki, "TRELLIS+: An effective approach for indexing genome-scale sequences using suffix trees," Proc. Pacific Symp. on Biocomputing, pp.90-101, Kohala Coast, Hawaii, Jan. 2008.
20. E. Rocke, "Using Suffix trees for gapped motif discovery," Proc. Annual Symp. on Combinatorial Pattern Matching (CPM), pp.335-349, Montreal, Canada, June 2000.
21. R. Sinha, S. Puglisi, A. Moffat, and A. Turpin, "Improving suffix array locality for fast pattern matching on disk," Proc. Int'l Conf. on Management of Data, ACM SIGMOD, pp.661-672, Vancouver, Canada, June 2008.
22. Y. Tian, S. Tata, R.A. Hankins, and J.M. Patel, "Practical methods for constructing suffix trees," VLDB Journal, vol.14, no.3, pp.281-299, 2005. (Pubitemid 41396781)
23. E. Ukkonen, "On-line construction of suffix trees," Algorithmica, vol.14, no.3, pp.249-260, Sept. 1995.
24. J.-I. Won, S.-K. Hong, J.-H. Yoon, S. Park, and S.-W. Kim, "A practical method for approximate subsequence search in DNA databases," Proc. Pacific-Asia Conf. on Advances in Knowledge Discovery and Data Mining (PAKDD), pp.921-931, Nanjing, China, May 2007.