A comparative genome approach to marker ordering

Abstract

The comparative mapping approach is available in the last version of de Givry,S. et al. [(2004) Bioinformatics, 21, 1703-1704, www.inra.fr/mia/T/CarthaGene], a free (the LKH part is free for academic use only) mapping software in C++, including LKH (Helsgaun,K. (2000) Eur. J. Oper. Res., 126, 106-130, www.dat.ruc.dk/keld/research/LKH) for maximum likelihood computation.

Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals

“…In the process of selecting the best map, this has particularly the effect of exploiting 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. This approach has proven to work well on both simulated and real data [Faraut et al, 2007;Marques et al, 2007;Prasad et al, 2007].…”

“…Indeed, having at hand a closely related completely sequenced genome allows taking advantage of the conservation of chromosome segments and the principle of comparative mapping to propose optimal orders. This idea has been developed within a statistical model by Faraut et al [2007], which uses the prior information of the order of a closely related genome together with the RH data to construct a criterion for comparing orders. In the process of selecting the best map, this has particularly the effect of exploiting 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.…”

“…This will specifically allow ranking the inconsistencies with respect to map uncertainty measures. Using statistical techniques such as MCMC (Monte Carlo Markov Chain), the model developed by Faraut et al [2007] can be used to estimate the uncertainty on the best map produced [Servin et al, in preparation] and distinguish regions where the RH map is possibly weak (i.e., other orders are possible) from regions where the RH map order is strongly supported. This allows pinpointing the discrepancies between the RH map and the sequence assembly for which the map order is well supported by the experimental mapping data, and therefore the sequence assembly is likely to be wrong.…”

A comparative radiation hybrid map of sheep chromosome 10

“…In this study, we have also tried to construct a map of OAR10 using a comparative RH mapping approach recently introduced in Cartha Gene (de Givry et al, 2005). This approach is based on a probabilistic Bayesian model integrating the usual RH probabilistic model with a probabilistic model of breakpoint occurrences with a reference order, typically obtained from the position of orthologous markers in a related sequenced genome (Faraut et al, 2007). In this probabilistic model, breakpoints induced by chromosomal rearrangements are considered as rare events, which follow a Poisson law.…”

An algorithm for solving the longest increasing circular subsequence problem

“…The LICS problem is a generalization of a classic longest increasing subsequence (LIS) problem, with applications in several areas, e.g., research on genomes [5] and as a tool for solving the widely known longest common subsequence problem [6]. The proved worst-case time lower bound for LIS is Ω(n log n) in the comparison model [6].…”