Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part IV: Incorporation of substitutions and other mutations

BioRxiv : the Preprint Server for Biology
Kiyoshi EzawaGiddy Landan

Abstract

Background Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. In a separate paper (Ezawa, Graur and Landan 2015a), we established the theoretical basis of our ab initio perturbative formulation of a continuous-time Markov model of the evolution of an entire sequence via insertions and deletions along time axis. In other separate papers (Ezawa, Graur and Landan 2015b,c), we also developed various analytical and computational methods to concretely calculate alignment probabilities via our formulation. In terms of frequencies, however, substitutions are usually more common than indels. Moreover, many experiments suggest that other mutations, such as genomic rearrangements and recombination, also play some important roles in sequence evolution. Results Here, we extend our ab initio perturbative formulation of a genuine evolutionary model so that it can incorporate other mutations. We give a sufficient set of conditions that the probability of evolution via both indels and substituti...Continue Reading

Related Concepts

Part
Genome
Recombination, Genetic
Gene Deletion
Genomics
Nucleotides
Local
Base Sequence
DNA Sequence Rearrangement
Gene Rearrangement

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