Coalescent framework for prokaryotes undergoing interspecific homologous recombination

Designing E1 Deleted Adenoviral Vector by Homologous Recombination

Adenoviruses are used extensively to deliver genes into mammalian cells, particularly where there is a requirement for high-level expression of transgene products in cultured cells, or for use as recombinant viral vaccines or in gene therapy. In spite of their usefulness, the construction of adenoviral vectors (AdV) is a cumbersome and lengthy process that is not readily amenable to the generat...

The coalescent with recombination

Homologous recombination is involved in the diversity of replacement flexible genomic islands in aquatic prokaryotes

Different strains of the same prokaryotic species, even very similar ones, vary in large regions of their genomes. This flexible genome represents a huge reservoir of diversity that allows prokaryotes to exploit their environment efficiently. Most of the flexible genome is concentrated in genomic islands, some of which are present in all the strains and coding for similar functions but containi...

Coalescent simulation of intracodon recombination.

The coalescent with recombination is a very useful tool in molecular population genetics. Under this framework, genealogies often represent the evolution of the substitution unit, and because of this, the few coalescent algorithms implemented for the simulation of coding sequences force recombination to occur only between codons. However, it is clear that recombination is expected to occur most...

Approximating the coalescent with recombination.

The coalescent with recombination describes the distribution of genealogical histories and resulting patterns of genetic variation in samples of DNA sequences from natural populations. However, using the model as the basis for inference is currently severely restricted by the computational challenge of estimating the likelihood. We discuss why the coalescent with recombination is so challenging...