Abstract
A method is discussed for DNA or protein sequence comparison using a finite field fast Fourier transform, a digital signal processing technique; and statistical methods are discussed for analyzing the output of this algorithm. This method compares two sequences of length N in computing time proportional to N log N compared to N2 for methods currently used. This method makes it feasible to compare very long sequences. An example is given to show that the method correctly identifies sites of known homology.
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Selected References
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- Felsenstein J., Sawyer S., Kochin R. An efficient method for matching nucleic acid sequences. Nucleic Acids Res. 1982 Jan 11;10(1):133–139. doi: 10.1093/nar/10.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
- Lipman D. J., Wilbur W. J., Smith T. F., Waterman M. S. On the statistical significance of nucleic acid similarities. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):215–226. doi: 10.1093/nar/12.1part1.215. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maizel J. V., Jr, Lenk R. P. Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7665–7669. doi: 10.1073/pnas.78.12.7665. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443–453. doi: 10.1016/0022-2836(70)90057-4. [DOI] [PubMed] [Google Scholar]
- Wilbur W. J., Lipman D. J. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 1983 Feb;80(3):726–730. doi: 10.1073/pnas.80.3.726. [DOI] [PMC free article] [PubMed] [Google Scholar]