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- COMPARATIVE GENOMICS , 2000
- Genome Biol
- J UROL , 2001
"... Comparative genome maps are a powerful tool for understanding the genomes of related organisms. Construction of any genetic map is laborious, but compiling comparative maps across multiple species requires a large investment of manual effort on the part of biologists. Additionally, biologists from d ..."
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Comparative genome maps are a powerful tool for understanding the genomes of related organisms. Construction of any genetic map is laborious, but compiling comparative maps across multiple species requires a large investment of manual effort on the part of biologists. Additionally, biologists from different labs often use differing rules that are not fully specified or made precise in the literature, making it difficult to understand how thevarious comparative maps relate to one another. We have formalized the construction of comparative maps as a chromosome labeling problem, providing a rigorous mathematical framework upon which we can build mathematical models. We offer an explicit set of principles on which to base models for the construction of such maps. We have developed broadly applicable models that emphasize the global similarities important in tracing chromosome evolution and de-emphasize lower-level differences, and we present efficient algorithms that allow us to automate this effort. We demonstrate the usefulness of these methods on diverse pairs of species, and on species maps with widely differing resolutions. We show that these methods produce biologically meaningful comparative maps which are quite similar to comparative maps previously published in the biological literature. Our approach is robust to errors and ambiguities in the underlying species map data such as marker order. When the input marker order is not resolved, we can arrange the co-located markers to produce a most parsimonious comparative map. We have incorporated our algorithms into an open source product named "DeCAL" (Detecting Common Ancestral Linkage-segments) which constructs comparativemaps within a few minutes on a standard UNIX workstation.