Section: New Results

Genome rearrangements

• A. Thomas has started his PhD on September 2011. We already obtained two results:

  • We designed an algorithm for finding the minimal number of block interchanges required to transform a duplicated linear genome into a tandem duplicated linear genome. We provide a formula for the distance as well as a polynomial time algorithm for the sorting problem. This work has been accepted in Bioinformatics 2012.

  • We also introduced and study a new combinatorial problem, a biological phenomenon that apparently associates a significant proportion of segmental duplications in mammalians, drosophilas and bacterias to breakpoints in rearrangement events. called the Genome Dedoubling Problem. It consists in finding a minimum length rearrangement scenario required to transform a genome with duplicated segments into a non-duplicated genome such that duplications are caused by rearrangement breakpoints. We introduced new graph data structures to solve these problems. This work was presented at RECOMB'CG 2011 [11]

• We designed and applied new algorithms for infering ultra-perfect evolution scenarios for Drosophila and mammals species [6] .

• We implemented and applied the algorithm of [32] for the reconstruction of species tree from gene trees of Fungal and eukaryotes species [8] .

• We proposed a new reconstruction of the architecture of the ancestral amniote genome based on the detection and assembly of ancestral genomic features conserved in extant species [9] .