Abstract
In this paper, we study the problem of sequence similarity search. We incorporate vector transformations and apply DFT (Discrete Fourier Transformation) and DWT (Discrete Wavelet Transformation, Haar) dimensionality reduction techniques to reduce the search space/time of sequence similarity range queries. Our empirical results on a number of Prokaryote and Eukaryote DNA contig databases demonstrate up to 50-fold filtration ratio reduction of the search space and up to 13 times faster filtration. The proposed transformation techniques may easily be integrated as a pre-processing phase on top of current similarity search heuristics/techniques such as BLAST, PatternHunter, FastA and QUASAR to efficiently prune non-relevant sequences. We study the precision of applying dimensionality reduction techniques for faster and more efficient range query searches and discuss the imposed trade-offs.
| Original language | English |
|---|---|
| Pages (from-to) | 733-754 |
| Number of pages | 22 |
| Journal | International Journal on Artificial Intelligence Tools |
| Volume | 14 |
| Issue number | 5 |
| DOIs | |
| Publication status | Published - 1 Oct 2005 |
| Externally published | Yes |
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Keywords
- Biological databases
- Range query
- Sequence similarity
- Sequence transformation
- String comparison
ASJC Scopus subject areas
- Artificial Intelligence
Cite this
Sequence similarity search using discrete fourier and wavelet transformation techniques. / Aghili, S. Alireza; Agrawal, Divyakant; El Abbadi, Amr.
In: International Journal on Artificial Intelligence Tools, Vol. 14, No. 5, 01.10.2005, p. 733-754.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Sequence similarity search using discrete fourier and wavelet transformation techniques
AU - Aghili, S. Alireza
AU - Agrawal, Divyakant
AU - El Abbadi, Amr
PY - 2005/10/1
Y1 - 2005/10/1
N2 - In this paper, we study the problem of sequence similarity search. We incorporate vector transformations and apply DFT (Discrete Fourier Transformation) and DWT (Discrete Wavelet Transformation, Haar) dimensionality reduction techniques to reduce the search space/time of sequence similarity range queries. Our empirical results on a number of Prokaryote and Eukaryote DNA contig databases demonstrate up to 50-fold filtration ratio reduction of the search space and up to 13 times faster filtration. The proposed transformation techniques may easily be integrated as a pre-processing phase on top of current similarity search heuristics/techniques such as BLAST, PatternHunter, FastA and QUASAR to efficiently prune non-relevant sequences. We study the precision of applying dimensionality reduction techniques for faster and more efficient range query searches and discuss the imposed trade-offs.
AB - In this paper, we study the problem of sequence similarity search. We incorporate vector transformations and apply DFT (Discrete Fourier Transformation) and DWT (Discrete Wavelet Transformation, Haar) dimensionality reduction techniques to reduce the search space/time of sequence similarity range queries. Our empirical results on a number of Prokaryote and Eukaryote DNA contig databases demonstrate up to 50-fold filtration ratio reduction of the search space and up to 13 times faster filtration. The proposed transformation techniques may easily be integrated as a pre-processing phase on top of current similarity search heuristics/techniques such as BLAST, PatternHunter, FastA and QUASAR to efficiently prune non-relevant sequences. We study the precision of applying dimensionality reduction techniques for faster and more efficient range query searches and discuss the imposed trade-offs.
KW - Biological databases
KW - Range query
KW - Sequence similarity
KW - Sequence transformation
KW - String comparison
UR - http://www.scopus.com/inward/record.url?scp=33746208831&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33746208831&partnerID=8YFLogxK
U2 - 10.1142/S0218213005002363
DO - 10.1142/S0218213005002363
M3 - Article
AN - SCOPUS:33746208831
VL - 14
SP - 733
EP - 754
JO - International Journal on Artificial Intelligence Tools
JF - International Journal on Artificial Intelligence Tools
SN - 0218-2130
IS - 5
ER -