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Nucleic Acids Res. 1990 Nov 11; 18(21): 6305–6310.
PMCID: PMC332496

Fourier methods for biosequence analysis.


Novel methods are discussed for using fast Fourier transforms for DNA or protein sequence comparison. These methods are also intended as a contribution to the more general computer science problem of text search. These methods extend the capabilities of previous FFT methods and show that these methods are capable of considerable refinement. In particular, novel methods are given which (1) enable the detection of clusters of matching letters, (2) facilitate the insertion of gaps to enhance sequence similarity, and (3) accommodate to varying densities of letters in the input sequences. These methods use Fourier analysis in two distinct ways. (1) Fast Fourier transforms are used to facilitate rapid computation. (2) Fourier expansions are used to form an 'image' of the sequence comparison.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Felsenstein J, Sawyer S, Kochin R. An efficient method for matching nucleic acid sequences. Nucleic Acids Res. 1982 Jan 11;10(1):133–139. [PMC free article] [PubMed]
  • Benson DC. Digital signal processing methods for biosequence comparison. Nucleic Acids Res. 1990 May 25;18(10):3001–3006. [PMC free article] [PubMed]
  • Karlin S, Altschul SF. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A. 1990 Mar;87(6):2264–2268. [PMC free article] [PubMed]
  • Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. [PMC free article] [PubMed]

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