A comparative genome approach to marker ordering

T. Faraut, S. de Givry, P. Chabrier, T. Derrien, F. Galibert, C. Hitte, T. Schiex
2007 Bioinformatics  
The increased number of genomes being sequenced offers new opportunities for the mapping of closely related organisms. We propose an algorithmic formalization of a genome comparison approach to marker ordering. In order to integrate a comparative mapping approach in the algorithmic process of map construction and selection, we extend the usual statistical model describing the experimental data, here radiation hybrids (RH) data, in a statistical framework that models additionally the
more » ... relationships between a proposed map and a reference map: an existing map of the corresponding orthologous genes or markers in a closely related organism. This has concretely the effect of exploiting, in the process of map selection, the information of marker adjacencies in the related genome when the information provided by the experimental data is not conclusive for the purpose of ordering. In order to compute efficiently the map, we proceed to a reduction of the maximum likelihood estimation to the Traveling Salesman Problem. Experiments on simulated RH data sets as well as on a real RH data set from the canine RH project show that maps produced using the likelihood defined by the new model are significantly better than maps built using the traditional RH model.
doi:10.1093/bioinformatics/btl321 pmid:17237105 fatcat:5mzpfdseubdsbkl7mls4tknlnq