Piers: An efficient model for similarity search in DNA sequence databases

SIGMOD Record

Volumn 33, Issue 2, 2004, Pages 39-44

  Cao, Xia ^a   Li, Shuai Cheng ^a   Ooi, Beng Chin ^a   Tung, Anthony K H ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTATIONAL METHODS; DATABASE SYSTEMS; DNA SEQUENCES; DYNAMIC PROGRAMMING; GENES; MATHEMATICAL MODELS;

BIOLOGICAL DATABASES; PIER MODEL; SEQUENCE SEARCH;

BIOTECHNOLOGY;

EID: 4444248319     PISSN: 01635808     EISSN: None     Source Type: Journal    
DOI: 10.1145/1024694.1024701     Document Type: Conference Paper

References (17)

1. S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman. A basic local alignment search tool. In Journal of Molecular Biology, 1990.
2. S. Burkhardt, A. Crauser, P. Ferragina, H. P. Lenhof, and M. Vingron. q-gram based database searching using a suffix array (quasar). In Int. Conf. RECOMB, Lyon, April 1999.
3. C. Faloutsos, M. Ranganathan, and Y. Manolopoulos. Fast subsequence matching in time-series databases. In Proc. 1994 ACM-SIGMOD Int. Conf. Management of Data (SIGMOD'94), pages 419-429, Minneapolis, Minnesota, May 1994.
4. E. Giladi, M. Walker, J. Wang, and W. Volkmuth. Sst: An algorithm for searching sequence databases in time proportional to the logarithm of the database size. In Int. Conf. RECOMB, Japan, 2000.
5. D. Gusfield. Algorithms on Strings, Trees and Sequences, Computer Science and Computation Biology. Cambridge University Press, New York, 1997.
6. E. Hunt, M. P. Atkinson, and R. W. Irving. A database index to large biological sequences. In International Journal on VLDB, pages 139-148, Roma, Italy, September 2001.
7. T. Kahveci and A. Singh. An efficient index structure for string databases. In Int. Conf. VLDB, Roma, Italy, 2001.
8. B. Ma, J. Tromp, and M. Li. Patternhunter: faster and more sensitive homology search. Bioinformatics, 18:440-445, 2002.
9. U. Manber and G. Myers. Suffix arrays: a new method for on-line string search. SIAM Journal on Computing, 22:935-948, 1993.
10. C. Meek, J.M. Patel, and S. Kasetty. Oasis: An online and accurate technique for local-alignment searches on biological sequences. In Proc. 2003 Int. Conf. Very Large Data Bases (VLDB'03), pages 910-921, Berlin, Germany, Sept. 2003.
11. S. Muthukrishnan and S.C. Sahinalp. Approximate nearest neighbors and sequence comparison with block operation. In STOC,Portland, Or, 2000.
12. O. Ozturk and H. Ferhatosmanoglu. Effective indexing and filtering for similarity search in large biosequence datasbases. In Third IEEE Symposium on BioInformatics and BioEngineering (BIBE'03), Bethesda, Maryland, 2003.
13. W.R. Pearson and D.J. Lipman. Improved tools for biological sequence comparison. Proceedings Natl. Acad. Sci. USA, 85:2444-2448, 1988.
14. T.F. Smith and M.S. Waterman. Identification of common molecular subsequences. Molecular Biology, 147:195-197, 1981.
15. Z. Tan, X. Cao, B.C. Ooi, and A. Tung. The ed-tree: an index for large dna sequence databases. In In Proc. 15th Int. Conf. on Scientific and Statistical Database Management, pages 151-160, 2003.
16. P. Weiner. Linear pattern matching algorithms. In Proc. 14th IEEE Symp. On Switching and Automata Theory, pages 1-11, 1973.
17. H.E. Williams and J.Zobel. Indexing and retrieval for genomic databases. IEEE Transactions on Knowledge and Data Engineering, 14:63-78, 2002.