Filtration of string proximity search via transformation

S. Alireza Aghili, Divyakant Agrawal, Amr El Abbadi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Citations (Scopus)

Abstract

The problem of proximity search in biological databases is addressed. We study vector transformations and conduct the application of DFT(Discrete Fourier Transformation) and DWT(Discrete Wavelet Transformation, Haar) dimensionality reduction techniques for DNA sequence proximity search to reduce the search time of range queries. Our empirical results on a number of Prokaryote and Eukaryote DNA contig databases demonstrate up to 50-fold filtration ratio of the search space, up to 13 times faster filtration. The proposed transformation techniques may easily be integrated as a preprocessing phase on top of the current existing similarity search heuristics such as BLAST[1], PattenHunter[11], FastA[17], QUASAR[4] and 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 languageEnglish
Title of host publicationProceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages149-157
Number of pages9
ISBN (Electronic)0769519075, 9780769519074
DOIs
Publication statusPublished - 1 Jan 2003
Event3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003 - Bethesda, United States
Duration: 10 Mar 200312 Mar 2003

Publication series

NameProceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003

Other

Other3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003
CountryUnited States
CityBethesda
Period10/3/0312/3/03

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ASJC Scopus subject areas

  • Computer Networks and Communications
  • Signal Processing
  • Electrical and Electronic Engineering

Cite this

Aghili, S. A., Agrawal, D., & Abbadi, A. E. (2003). Filtration of string proximity search via transformation. In Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003 (pp. 149-157). [1188941] (Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBE.2003.1188941