Algorithm for statistical alignment of two sequences derived from a Poisson sequence length distribution

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Abstract

The statistical approach to DNA sequence evolution involves the stochastic modelling of the substitution, insertion and deletion processes. Substitution has been modelled by finite Markov-process for more than three decades. Modelling the insertion and deletion process is in its new-age, and the recent model has a serious drawback: it assumes geometric sequence length equilibrium distribution, which contradicts biological knowledge. An algorithm is presented that computes the joint probability of two sequences evolved on a non-reversible way from a Poisson sequence length distribution.

Original languageEnglish
Pages (from-to)79-84
Number of pages6
JournalDiscrete Applied Mathematics
Volume127
Issue number1 SPEC.
DOIs
Publication statusPublished - Apr 1 2003

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Keywords

  • Dynamic programming
  • Irreversible sequence evolution
  • Statistical alignment

ASJC Scopus subject areas

  • Discrete Mathematics and Combinatorics
  • Applied Mathematics

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