Sorting genomes by translocations and deletions.

A (1.408+ε)-Approximation Algorithm for Sorting Unsigned Genomes by Reciprocal Translocations

Memetic and Opposition-Based Learning Genetic Algorithms for Sorting Unsigned Genomes by Translocations

A standard genetic algorithm for sorting unsigned genomes by translocations is improved in two different manners: 1. a memetic algorithm (GAMA ) is provided, which embeds a new stage of local search, based on the concept of mutation applied in only one gene; 2. an oppositionbased learning (GAOBL ) mechanism is provided, which explores the concept of internal opposition applied to a chromosome. ...

SoRT2: a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations

SoRT(2) is a web server that allows the user to perform genome rearrangement analysis involving reversals, generalized transpositions and translocations (including fusions and fissions), and infer phylogenetic trees of genomes being considered based on their pairwise genome rearrangement distances. It takes as input two or more linear/circular multi-chromosomal gene (or synteny block) orders in...

A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions

A common approach in comparative genomics is to compare the order of appearance of orthologous genes in different genomes. Genomes are represented by permutations, where each element stands for a gene. Circular genomes (such as bacterial and mitochondrial genomes) are represented by circular permutations. The basic task is, given two permutations, to find a shortest sequence of rearrangement op...

log(n)) algorithm for sorting by reciprocal translocations

We prove that sorting by reciprocal translocations can be done in O(n3/2 √ log(n)) for an n-gene genome. Our algorithm is an adaptation of the algorithm of Tannier, Bergeron and Sagot for sorting by reversals. This improves over the O(n3) algorithm for sorting by reciprocal translocations given by Bergeron, Mixtacki and Stoye.