Homogenization of Tandemly Repeated Nucleotide Sequences by Distance-Dependent Nucleotide Sequence Conversion

Homogenization of tandemly repeated nucleotide sequences by distance-dependent nucleotide sequence conversion.

Previous work revealed that recurrent mutations (= mutation occurring more than once) in the tandemly repeated arrays present in nontranscribed spacers (NTS) of ribosomal RNA genes (rDNA) are clustered, i.e., they most frequently occur in repeats with adjacent or alternate distribution. A possible explanation is that the likelihood of heteroduplex formation, a prerequisite of gene conversion, d...

Estimation of evolutionary distance between nucleotide sequences.

A mathematical formula for estimating the average number of nucleotide substitutions per site (delta) between two homologous DNA sequences is developed by taking into account unequal rates of substitution among different nucleotide pairs. Although this formula is obtained for the equal-input model of nucleotide substitution, computer simulations have shown that it gives a reasonably good estima...

Unbiased estimation of evolutionary distance between nucleotide sequences.

A new algorithm for estimating the number of nucleotide substitutions per site (i.e., the evolutionary distance) between two nucleotide sequences is presented. This algorithm can be applied to many estimation methods, such as Jukes and Cantor's method, Kimura's transition/transversion method, and Tajima and Nei's method. Unlike ordinary methods, this algorithm is always applicable. Numerical co...

Evolution of Tandemly Repeated Sequences Through Duplication and Inversion

Given a phylogenetic tree T for a family of tandemly repeated genes and their signed order O on the chromosome, we aim to find the minimum number of inversions compatible with an evolutionary history of this family. This is the first attempt to account for inversions in an evolutionary model of tandemly repeated genes. We present a time-efficient branch-and-bound algorithm and show, using simul...

Nucleotide sequences in DNA