Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mecha...

Large genomes are full of repeated DNA sequences. It was estimated that over half of the human DNA consists of repeated sequences (Baltimore 2001; Eichler 2001; Leem et al. 2002). Tandem duplication is one of the important evolutionary mechanisms for producing repeated DNA sequences, in which the copies that may or may not contain genes are adjacent along the genome. Fitch (1977) first observed...

A tandem duplication of the mitochondrial tRNA(Thr) and tRNA(Pro) genes in the amphisbaenian reptile Bipes biporus is the first case reported of a tandem duplication restricted to a single pair of tRNA genes in a vertebrate mitochondrial genome. Such duplications have been predicted, however, as intermediate steps in the evolution of observed mitochondrial genomic rearrangements through errors ...

We develop a recurrence relation that counts the number of Tandem Duplication Trees (either rooted or unrooted) that are consistent with a set of n tandemly repeated sequences generated under the standard unequal recombination (or crossover) model of tandem duplications. We find that the number of rooted duplication trees is exactly twice the number of unrooted trees, which means, on average, o...

We developed a recurrence relation that counts the number of tandem duplication trees (either rooted or unrooted) that are consistent with a set of n tandemly repeated sequences generated under the standard unequal recombination (or crossover) model of tandem duplications. The number of rooted duplication trees is exactly twice the number of unrooted trees, which means that on average only two ...