Nucleic Acids Research

Figure 3. Visualizing maps with MappetShow.

In ZoomMap (11), HuGeMap is represented as a two-dimensional world where the user can travel by zooming in and out on objects. The starting point is a rough karyotype of the human genome (Fig. 1a). As the user zooms in, more details appear as chromosomes get closer and space becomes available. The arms of the chromosomes are visible on Figure 1b, later the cytogenetic banding and textual information (names of the maps of the chromosome) are displayed (Fig. 1c). When zooming in further, the name of the chromosome maps are replaced by the usual representation of a map (Fig. 1d) with more and more markers as scale increases (Fig. 1e). Finally the sequence appears (Fig. 1f).

In Figure 1e, the square boxes linked to a marker are portals which display another part of the HuGeMap world: they point to the other maps on which the marker is positioned. They allow the user to navigate directly to a related map.

The data represention used by ZoomMap can be modified by the use of magic lenses. These are dynamic items under user control that allow a transformation of the data display in the box defined by the lens. Figure 2a shows two lenses used to convert the chromosome banding into chromosome marker maps. In Figure 2b, the bottom lens displays the marker names using a grey scale depending on their polymorphism and the top lens gives more information on the markers. In Figure 2c, a lens that filters out the markers with low polymorphism has been stacked on the bottom lens.

ZoomMap was written with the Zomit package. It can be used with the Zomit Java applet client at http://www.infobiogen.fr/services/zomit/ZoomMap.html

MappetShow

MappetShow (Fig. 3) is a graphical interface, written in Java, that draws and compares maps (http://www.infobiogen.fr/services/Mappet ). The user can choose a chromosome or a marker. The maps related to the chromosome or containing the marker are listed and can be selected for display (Fig. 3a). Each displayed map can be browsed and scaled independently (Fig. 3c). When the user specifies a marker, all maps are recentred on this marker. MappetShow is also connected to the HuGeMap WWW browser (Fig. 3b).

In MappetShow we implemented a Focus+Context technique which shows a detailed view of the area of interest, while keeping a summary of the remaining data visible. This is performed with variable scaling. It allows the user to focus on the markers of interest of a map, while keeping a view of the context of the whole map.

Independent non-linear views facilitate browsing and graphical comparison of different maps on different regions (Fig. 3d).

PERSPECTIVES

Our intention is to integrate all mammalian genome maps with the human maps. MappetShow and ZoomMap will be modified to display the comparative maps. We will use our standard genome map IDL in the development of a mammalian genome database at Infobiogen and promote the use of this standard format in the mapping community under the auspices of the Object Management Group (http://www.omg.org ).

ACKNOWLEDGEMENTS

This work is partly granted by the EC contracts BIO4-CT95-0037 and BIO4-CT96-0346. We thank Frédéric Achard for his comments on the manuscript.

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*To whom correspondence should be addressed at: GIS Infobiogen, 7 rue Guy Môquet BP 8, 94801 Villejuif cedex, France. Tel: +33 1 49 58 36 82; Fax: +33 1 45 59 52 50; Email: manu@infobiogen.fr

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