Sequence similarity search using discrete fourier and wavelet transformation techniques

International Journal on Artificial Intelligence Tools

Volumn 14, Issue 5, 2005, Pages 733-754

  Aghili, S Alireza ^a   Agrawal, Divyakant ^a   El Abbadi, Amr ^a  

^a University of California   (United States)

Author keywords

Biological databases; Range query; Sequence similarity; Sequence transformation; String comparison

Indexed keywords

EID: 33746208831     PISSN: 02182130     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0218213005002363     Document Type: Article

References (25)

1. S.A. Aghili, D. Agrawal and A. El Abbadi, Efficient Filtration of Sequence Similarity Search Through Singular Value Decomposition, (BIBE 2004), pp. 403-410.
2. S.A. Aghili, D. Agrawal and A. El Abbadi, BFT: Bit Filtration Technique for Approximate String Join in Biological Databases, (SPIRE 2003), pp. 326-340.
3. S.A. Aghili, D. Agrawal and A. El Abbadi, Filtration of String Proximity Search via Transformation, (BIBE 2003), pp. 149-157.
4. S. Altschul, W. Gish, W. Miller, E. Myers and D. J. Lipman, Basic Local Alignment Search tool, (Journal of Molecular Biology 1990(215)), pp. 403-410.
5. A. Apostolico, The myriad virtues of subword trees, (Combinatorial Algorithms on Words, NATO ISI Series, Springer-Verlag 1985), pp. 85-96.
6. A.D. Baxevanis and B.F. Francis Ouellette, Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, (Wiley Interscience 2001).
7. Stefan Burkhardt, Andreas Crauser, Paolo Ferragina, Hans-Peter Lenhof, Éric Rivals and Martin Vingron, q-gram Based Database Searching Using a Suffix Array (QUASAR), (RECOMB 1999), pp. 77-83.
8. E. Chavez and G. Navarro, A Metric Index for Approximate String Matching, (LATIN 2002), pp. 181-195.
9. M.O. Dayhoff, R.M. Schwartz and B.C. Orcutt, A model of evolutionary change in proteins, (Atlas of Protein Sequence Structure. National Biomedical Research Foundation, Washington, DC 1978(5)), pp. 345-352.
10. E. Giladi, M. G. Walker, J.Z. Wang and W. Volkmuth, SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size, (Bioinformatics 2002(18)(6)), pp. 873-877.
11. S. Henikoff and J.G. Henikoff, Amino acid substitution matrices from protein blocks, (Proceedings National Academy of Science 1992(89)), pp. 10915-10519.
12. P. Jokinen and E. Ukkonen, Two Algorithms for Approximate String Matching in Static Texts, (Proceedings of MFCS 1991(16)), pp. 240-248.
13. T. Kahveci and A.K. Singh, Efficient Index Structures for String Databases, (VLDB 2001), pp. 351-360.
14. B. Ma, J. Tromp and M. Li, PatternHunter: faster and more sensitive homology search, (Bioinformatics 2002(18)(3)), pp. 440-445.
15. Carl D. Meyer, Matrix Analysis and Applied Linear Algebra, (SIAM, Philadelphia, 2000).
16. G. Navarro and R.A. Baeza-Yates, A hybrid indexing method for approximate string matching, (Journal of Discrete Algorithms 2000(1)(1)), pp. 205-239.
17. G. Navarro, R.A. Baeza-Yates, E. Sutinen and J. Tarhio, Indexing Methods for Approximate String Matching, (IEEE Data Engineering Bulletin 2001(24)(4)), pp. 19-27.
18. NCBI, National Center for Biotechnology Information(NCBI) website, (http://www.ncbi.nih.gov/).
19. S.B. Needleman and C.D. Wunsch, General method applicable to the search for similarities in the amino acid sequence of two proteins, (Journal of Molecular Biology 1970(48)), pp. 443-453.
20. W.R. Pearson, Using the 5 program, to search protein and DNA sequence databases, (Methods in Molecular Biology 1994(25)), pp. 365-389.
21. R. Smith and M.S. Waterman, Identification of common molecular subsequences, (Journal of Molecular Biology 1981(148)), pp. 195-197.
22. J. D. Thompson, D.G. Higgins and T.J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice, (Nucleic Acids Research 1994(22)), pp. 4673-4680.
23. University of Chicago's Howard Hughes Medical Institute, New type of DNA-free inheritance in yeast is spread by a madcow mechanism, (http://www.uchospitals.edu/news/1997/19970530-prion-fibers.html).
24. D. Wheeler, Weight Matrices for Sequence Similarity Scoring, (http://www.techfak.uni-bielefeld.de/bcd/Curric/PrwAli/nodeD.html).
25. Y. Wu, D. Agrawal and A. El Abbadi, A Comparison of DFT and DWT based Similarity Search in Time-Series Databases, (CIKM 2000), pp. 488-495.