NDLI: Using signal processing techniques for DNA sequence comparison

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Proceedings of the 1988 Fourteenth Annual Northeast Bioengineering Conference

Using signal processing techniques for DNA sequence comparison

Content Provider	IEEE Xplore Digital Library
Author	Cheever, E.A. Searls, D.B. Karunaratne, W. Overton, G.C.
Copyright Year	1989
Description	Author affiliation: Dept. of Eng., Swarthmore Coll., PA, USA (Cheever, E.A.; Searls, D.B.; Karunaratne, W.; Overton, G.C.)
Abstract	The most widely used algorithm for the comparison of two sequences of DNA are O(m*n) on the lengths, m and n, of the sequences been compared. The authors present a comparison algorithm that is O(nlog n) on the length, n, of the longer sequence. This algorithm uses techniques developed for rapid comparison of two discrete signals, in particular, cross-correlation using the fast Fourier transform (FFT). The authors treat the DNA as a discrete signal with each nucleotide base represented by a single point in the signal. There are only four possible values that the signal can assume which they represent by one of four complex numbers. The comparison is made by performing a cross correlation between one signal and the complex conjugate of the other. Any significant peak in the resulting signal indicates a strong similarity between the two sequences. The authors present the results of comparison of two strains of the human immunodeficiency virus and of human and simian immunodeficiency viruses. Their results suggest that this technique is a powerful method for comparing very long sequences of DNA.<>
Starting Page	173
Ending Page	174
File Size	219927
Page Count	2
File Format	PDF
DOI	10.1109/NEBC.1989.36756
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	1989-03-27
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Signal processing DNA Sequences Signal processing algorithms Humans Genomics Bioinformatics Fourier transforms Fast Fourier transforms Educational institutions
Content Type	Text
Resource Type	Article

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