Filtration of String Proximity Search via Transformation

The problem of proximity search in biological databases is addressed. We study vectortransformations and conduct the application of DFT(Discrete Fourier Transformation) andDWT(Discrete Wavelet Transformation, Haar) dimensionality reduction techniques for DNAsequence proximity search to reduce the search time of range queries. Our empirical results on anumber of Prokaryote and Eukaryote DNA contig databases demonstrate up to 50-fold filtrationratio of the search space, up to 13 times faster filtration. The proposed transformation techniquesmay easily be integrated as a preprocessing phase on top of the current existing similarity searchheuristics such as BLAST[1], PattenHunter[3], FastA[4], QUASAR[2] and to efficiently prunenon-relevant sequences. We study the precision of applying dimensionality reduction techniquesfor faster and more efficient range query searches, and discuss the imposed trade-offs. References[1] S. Altschul, W. Gish, W. Miller, E. Myers, and D. J. Lipman. Basic local alignment search tool. J. Mol. Biol.,215:403–410, 1990.[2] S. Burkhardt, A. Crauser, P. Ferragina, H.P. Lenhof, E. Rivals, and M. Vingron. q-gram based database searchingusing a suffix array (quasar). In RECOMB, pages 77–83, 1999.[3] B. Ma, J. Tromp, and M. Li. Patternhunter: faster and more sensitive homology search. Bioinformatics, 18(3):440–445, March 2002.[4] W. R. Pearson. Using the fasta program to search protein and dna sequence databases. Methods Mol Biol,25:365–389, 1994.