A COMPARATIVE GENOME MAPPING TOOL

National Center for Genome Resources, 1800A Old Pecos Trail, Santa Fe, New Mexico 87505

NCGR's Comparative Genome Mapping Tool (prototype) is a software package used in combination with genome map datasets to display relationships between and among genetic linkage maps and/or physical maps for the same or related species. Individual maps appear as scaled line segments with mapped objects color-coded by type, and sized according to assigned confidence levels. Relationships between mapped objects are depicted as connecting lines, and underlying data is available via the mouse and cursor. Connections between mapped objects may be based on known relationships such as orthologous markers, or on suspected relationships such as name similarity, nomenclature mapping or sequence similarity. These genome map comparisons can provide many uses. For evolutionary studies, map comparisons provide insight into genome rearrangement and phylogenetic distance. Aligned genetic and physical maps for the same species are used to direct the physical search for genes. Quantitative Trait Loci (QTLs) can be compared across species by connecting orthologous markers which punctuate their spans. NCGR has acquired genome datasets for maize and rice and is using these to validate the tool and investigate new features.