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Distribution of the number of matches between nucleotide sequences

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Abstract

When two strings of symbols are aligned it is important to know whether the observed number of matches is better than that expected between two independent sequences with the same frequency of symbols. When strings are of different lengths, nulls need to be inserted in order to align the sequences. One approach is to use simple approximations of sampling for replacement. We describe an algorithm for exactly determining the frequencies of given numbers of matches, sampling without replacement. This does not lead to a simple closed form expression. However we show examples where sampling with, or without, replacement give very similar results and the simple approach may be adequate for all but the smallest cases.

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Author notes

  1. Ingrid Rinsma

    Present address: Dept of Mathematics and Statistics, Waikoto University, Hamilton, New Zealand

Authors and Affiliations

  1. Department of Mathematics and Statistics, Massey University, Palmerston North, New Zealand

    Ingrid Rinsma & Michael Hendy

  2. Department of Botany and Zoology, Massey University, Palmerston North, New Zealand

    David Penny

Authors
  1. Ingrid Rinsma
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  2. Michael Hendy
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  3. David Penny
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Rinsma, I., Hendy, M. & Penny, D. Distribution of the number of matches between nucleotide sequences. Bltn Mathcal Biology 52, 349–358 (1990). https://doi.org/10.1007/BF02458576

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  • DOI: https://doi.org/10.1007/BF02458576

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