Algorithms for the Extraction of Synteny Blocks from Comparative Maps

Abstract

In comparing genomic maps, we try to distinguish mapping errors and incorrectly resolved paralogies from genuine rearrangements of the genomes. This can be formulated as a Maximum Weight Independent Set (MWIS) search, where vertices are potential strips of markers syntenic on both genomes, and edges join conflicting strips, in order to extract the subset of compatible strips that accounts for the largest proportion of the data. This technique is computationally hard. We introduce biologically meaningful constraints on the strips, reducing the number of vertices for the MWIS analysis and provoking a decomposition of the graph into more tractable components. New improvements to existing MWIS algorithms greatly improve running time, especially when the strip conflicts define an interval graph structure. A validation of solutions through genome rearrangement analysis enables us to identify the most realistic solution. We apply this to the comparison of the rice and sorghum genomes.