Abstract
A query to a nucleotide database is a DNA sequence. Answers are similar sequences, that is, sequences with a high-quality local alignment. Existing techniques for finding answers use exhaustive search, but it is likely that, with increasing database size, these algorithms will become prohibitively expensive. We have developed a partitioned search approach, in which local alignment string matching techniques are used in tandem with an index. We show that fixedlength substrings, or intervals, are a suitable basis for indexing in conjunction with local alignment on likely answers. By use of suitable compression techniques the index size is held to an acceptable level, and queries can be evaluated several times more quickly than with exhaustive search techniques.
This is a preview of subscription content, log in via an institution.
Preview
Unable to display preview. Download preview PDF.
References
S. Altschul, M. Boguski, W. Gish, and J. Wootton. Issues in searching molecular sequence databases. Nature Genetics, 6:119–129, 1994.
S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman. Basic local alignment search tool. Journal of Molecular Biology, 215:403–410, 1990.
S.F. Altschul. A protein alignment scoring system sensitive at all evolutionary distances. Journal of Molecular Evolution, 36:290–300, 1993.
D. Benson, D.J. Lipman, and J. Ostell. GenBank. Nucleic Acids Research, 21(13):2963–2965, 1993.
M.J. Cinkosky, J.W. Fickett, P. Gilna, and C. Burks. Electronic data publishing in Genbank. Science, 252:1273–1277, 1991.
F. Collins and D. Galas. A new five-year plan for the US human genome project. Science, 262:43–46, 1993.
P. Elias. Universal codeword sets and representations of the integers. IEEE Transactions on Information Theory, IT-21(2):194–203, March 1975.
S.W. Golomb. Run-length encodings. IEEE Transactions on Information Theory, IT-12(3):399–401, July 1966.
D.E. Knuth, J.H. Morris, and V.R. Pratt. Fast pattern matching in strings. SIAM Journal of Computing, 6:323–350, 1977.
D.J. Lipman and W.R. Pearson. Rapid and sensitive protein similarity searches. Science, 227:1435–1441, 1985.
A. Moffat. Economical inversion of large text files. Computing Systems, 5(2):125–139, Spring 1992.
A. Moffat and J. Zobel. Self-indexing inverted files for fast text retrieval. ACM Transactions on Information Systems. (To appear).
A. Moffat and J. Zobel. Parameterised compression for sparse bitmaps. In Proc. ACM-SIGIR International Conference on Research and Development in Information Retrieval, pages 274–285, Copenhagen, Denmark, June 1992.
E.W. Myers. A sublinear algorithm for approximate keyword searching. Algorithmica. (To appear).
W.R. Pearson and D.J. Lipman. Improved tools for biological sequence comparison. Proc. National Academy of Science, 85:2444–2448, 1988.
C.M. Rice, R. Fachs, D.G. Higgins, P.J. Stoehr, and G.N. Cameron. The EMBL data library. Nucleic Acids Research, 21:2967–2971, 1993.
G. Salton. Automatic Text Processing: The Transformation, Analysis, and Retrieval of Information by Computer. Addison-Wesley, Reading, Massachusetts, 1989.
G. Salton and M.J. McGill. Introduction to Modern Information Retrieval. McGraw-Hill, New York, 1983.
D. Sankoff and J.B. Kruskal, editors. Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley, Reading, Massachusetts, 1983.
H. Williams and J. Zobel. Practical compression of nucleotide databases. In Proc. Australian Computer Science Conference, pages 184–193, Melbourne, Australia, 1996.
R. W. Williams. The portable dictionary of the mouse genome: a personal database for gene mapping and molecular biology. Mammalian Genome, 5:372–375, 1994.
J. Zobel and P. Dart. Finding approximate matches in large lexicons. Software-Practice and Experience, 25(3):331–345, March 1995.
J. Zobel, A. Moffat, and R. Sacks-Davis. Searching large lexicons for partially specified terms using compressed inverted files. In Proc. International Conference on Very Large Databases, pages 290–301, Dublin, Ireland, 1993.
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 1996 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Williams, H., Zobel, J. (1996). Indexing nucleotide databases for fast query evaluation. In: Apers, P., Bouzeghoub, M., Gardarin, G. (eds) Advances in Database Technology — EDBT '96. EDBT 1996. Lecture Notes in Computer Science, vol 1057. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0014158
Download citation
DOI: https://doi.org/10.1007/BFb0014158
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-61057-1
Online ISBN: 978-3-540-49943-5
eBook Packages: Springer Book Archive