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© IRL Press Limited

A test for the statistical significance of DNA sequence similarities for application in databank searches

R. F. Mott *, T. B. L. Kirkwood and R. N. Curnow 1

Laboratory of Mathematical Biology, National Institute for Medical Research Mill Hill, London NW7 IAA
1Department of Applied Statistics, University of Reading Reading RG6 2AN, UK

*To whom reprint requests should be sent

A method is developed, based on word-searching, which provides a rapid test for the statistical significance of DNA sequence similarities for use in databank searching. The method makes allowance for the lengths and dinucleotide compositions of the sequences being compared. A way is also described to calculate the power of the test, i.e. the probability of detecting a given similarity as being statistically significant. The effects on the power of the test of the scoring method, word length, sequence length, and sequence composition are examined. A novel scoring method is shown to be superior to the method currently used in most word-searching algorithms.

Received on August 3, 1988; accepted on December 12, 1988

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