相关论文: Expected number of inversions after a sequence of …
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as…
We give a new expression for the expected number of inversions in the product of n random adjacent transpositions in the symmetric group S_{m+1}. We then derive from this expression the asymptotic behaviour of this number when n scales with…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
We present a simple formula for the expected number of inversions in a permutation of size $n$ obtained by applying $t$ random (not necessarily adjacent) transpositions to the identity permutation. More general, for any finite irreducible…
Normal approximations for descents and inversions of permutations of the set $\{1,2,...,n\}$ are well known. A number of sequences that occur in practice, such as the human genome and other genomes, contain many repeated elements. Motivated…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
Genomic distance between two genomes, i.e., the smallest number of genome rearrangements required to transform one genome into the other, is often used as a measure of evolutionary closeness of the genomes in comparative genomics studies.…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
Permutations are usually enumerated by size, but new results can be found by enumerating them by inversions instead, in which case one must restrict one's attention to indecomposable permutations. In the style of the seminal paper by Simion…
Permutations are usually enumerated by size, but new results can be found by enumerating them by inversions instead, in which case one must restrict one's attention to indecomposable permutations. In the style of the seminal paper by Simion…
This paper proposes a new algorithm for generating all permutations of multisets. The method uses transpositions only and adjacent transpositions are favoured. The algorithm requires a strong homogeneous transposition condition:…
Motivated by applications in mathematical biology concerning randomly alternating motion of micro-organisms, we analyze a generalized integrated telegraph process. The random times between consecutive velocity reversals are…
Gene conversion is a mechanism by which a double-strand break in a DNA molecule is repaired using a homologous DNA molecule as a template. As a result, one gene is 'copied and pasted' onto the other gene. It was recently reported that the…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
Background. Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
In the context of the genome rearrangement problem, we analyze two well known models, namely the block transposition and the prefix block transposition models, by exploiting the connection with the notion of permutation pattern. More…