Protein domain repeats are common in proteins that are central to the organization of a cell, in particular in eukaryotes. They are known to evolve through internal tandem duplications. However, the understanding of the underlying mechanisms is incomplete. To shed light on repeat expansion mechanisms, we have studied the evolution of the muscle protein Nebulin, a protein that contains a large n...

In this work, we derive upper bounds on the cardinality of tandem and palindromic duplication correcting codes by deriving the generalized sphere packing bound for these error types. We first prove that an upper bound for tandem or palindromic deletions is also an upper bound for inserting the respective type of duplications. Therefore, we derive the bounds based on these special deletions as t...

We present a stochastic model for tandem duplications and point mutations that can be used to estimate relative mutation rates and the total number of mutations from a single sequence. Important parameters of the model include the probability of a point mutation and the probability of a tandem duplication of a given length. Our model indicates that if the probability of point mutations is insig...

One of the less well understood mutational transformations that act upon DNA is tandem duplication. In this process, a stretch of DNA is duplicated to produce two or more adjacent copies, resulting in a tandem repeat. Over time, the copies undergo additional mutations so that typically, multiple approximate tandem copies are present. An interesting feature of tandem repeats is that the duplicat...