Genomes as geography: using GIS technology to build interactive genome feature maps |
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Authors: | Mary E Dolan Constance C Holden M Kate Beard and Carol J Bult |
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Institution: | (1) National Center for Geographic Information and Analysis, University of Maine, Orono, ME 04469, USA;(2) The Jackson Laboratory, , Bar Harbor, ME 04609, USA |
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Abstract: | Background Many commonly used genome browsers display sequence annotations and related attributes as horizontal data tracks that can
be toggled on and off according to user preferences. Most genome browsers use only simple keyword searches and limit the display
of detailed annotations to one chromosomal region of the genome at a time. We have employed concepts, methodologies, and tools
that were developed for the display of geographic data to develop a Genome Spatial Information System (GenoSIS) for displaying
genomes spatially, and interacting with genome annotations and related attribute data. In contrast to the paradigm of horizontally
stacked data tracks used by most genome browsers, GenoSIS uses the concept of registered spatial layers composed of spatial
objects for integrated display of diverse data. In addition to basic keyword searches, GenoSIS supports complex queries, including
spatial queries, and dynamically generates genome maps. Our adaptation of the geographic information system (GIS) model in
a genome context supports spatial representation of genome features at multiple scales with a versatile and expressive query
capability beyond that supported by existing genome browsers. |
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