Computational protocol: Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes

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Protocol publication

[…] Ancestral syntenic blocks are reconstructed by a complex procedure that will be described in details elsewhere (M.Muffato et al., manuscript in preparation). Briefly, parsimonious scenarios are estimated based on pairwise comparisons of gene order between all available sequenced genomes (1378 comparisons in Genomicus v56.01). For a given ancestor, all ancestral genes that are identified as conserved neighbours in at least one such comparison become linked nodes in a graph. A weight (with values comprised between 1 and 1378) reflecting the number of times this situation was observed in all the comparisons is then applied to each link.At this stage, inconsistencies may appear in the form of ancestral genes connected to more than two neighbours. To resolve these, the weighted graph is processed using a top-down greedy algorithm where the links of highest weight are selected first and are used to select the most likely gene-to-gene connection in case of multiple choice.This produces a set of linear paths in the graph connecting ancestral genes based on the number of times their respective descendants are observed as extant neighbours. We performed extensive simulations and benchmarked our methods against several alternative methods: MGR (Bourque and Pevzner, ), MGRA (Alekseyev and Pevzner, ) and InferCars (Ma et al., ). Our method is the only approach able to satisfactorily analyse data with the volume (53 species and 888 217 extant genes) and complexity (duplications, deletions) found in the complete set of sequenced vertebrate genomes. The reconstructed gene order is correct in >95% of the cases (specificity), and includes between 70% and 95% of the expected ancestral gene pairs (sensitivity). […]

Pipeline specifications

Software tools MGR, MGRA, inferCars
Databases Genomicus
Application Phylogenetics