Finding all sorting tandem duplication random loss operations

Finding All Sorting Tandem Duplication Random Loss Operations

Finding All Tandem Arrays in DNA Sequences

A tandem array is a substring of the form k x , where x is any unspecific substring and k is at least two (when k is 2, 2 x is also called a tandem repeat or square). A non-extendable tandem array occurring in string S is a tandem array k x which are not followed or preceded by another occurrence of x in S. The problem of this thesis is defined as follows: Given a string S of length n, find all...

A variant of the tandem duplication - random loss model of genome rearrangement

In (4), Chaudhuri, Chen, Mihaescu and Rao study algorithmic properties of the tandem duplication random loss model of genome rearrangement, well-known in evolutionary biology. In their model, the cost of one step of duplication-loss of width k is αk for α = 1 or α ≥ 2. In this paper, we study a variant of this model, where the cost of one step of width k is 1 if k ≤ K and ∞ if k > K, for any va...

A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome.

Most reported examples of change in vertebrate mitochondrial (mt) gene order could be explained by a tandem duplication followed by random loss of redundant genes (tandem duplication-random loss [TDRL] model). Under this model of evolution, independent loss of genes arising from a single duplication in an ancestral species are predicted, and remnant pseudogenes expected, intermediate states tha...

Whole mirror duplication-random loss model and pattern avoiding permutations

a r t i c l e i n f o a b s t r a c t Keywords: Algorithms Combinatorial problems Pattern avoiding permutation Whole duplication-random loss model Genome Generating algorithm Binary reflected Gray code In this paper we study the problem of the whole mirror duplication-random loss model in terms of pattern avoiding permutations. We prove that the class of permutations obtained with this model af...