The display of comparative mapping data using ACEDB

# The One-to-Many Chromosome Map

The One-to-Many-Map, like the PairMap, is accessed through the Oxford Grid. It shows the homologies in one of the Oxford Grid's rows or columns. If a column is selected, then a chromosome (banding pattern) ideogram or numeric scale of the single Map of species 1 (at the top of the column) is placed alongside a grid of all the Maps of species 2. Homologies are drawn on the One-to-Many-Map as small blue boxes, their y-coordinates being their locations on the single Map and their x-coordinates being the centres of the columns that represent their relevant Maps in species 2. If an Oxford Grid row is selected, then conversely a single Map of species 2 is gridded against all Maps of species 1, in a similar way.

The y-axis of the One-to-Many-Map is labelled with a chromosome (banding pattern) ideogram, should this be available, or by a numeric scale. If the former, then all chromosome band names will be shown and these may be double-clicked to bring up text information on the bands. In either case the Map name will be shown in bold black text and may be double-clicked to bring up its graphical display. The x-axis is labelled with all the Map names of the relevant Map_set. The Map_set name is also shown in bold black text. All of these may be double clicked. For a Map name, this causes a graphical display of that Map to be produced. A text information box appears when the Map_set name is double-clicked.

The One-to-Many-Map shows the distribution of loci on a single Map in a particular species and their homologues throughout the Maps of another species. Conserved segments between the two species should become apparent as vertical lines of blue homology boxes. If two adjacent loci in a particular column are less than 25 map units apart, they are joined by a vertical Magenta line. This is hoped to help in the identification of conserved segments. In the future, it is hoped that this will become an option that can be turned on or off by the user and that the number of map units defining "closeness" will also be chosen by the user.

A special feature to highlight paralogy data is built within the One-to-Many-Map. If the loci involved in a particular homology on a One-to-Many-Map are also involved in another homology on the same One-to-Many-Map (paralogy data), then selecting the first homology (so that it is coloured light green) will cause the related homology to be coloured red, the relationship between them becoming clear to the user.

A single click on a blue box causes the names of the two homologous loci to be displayed in the light blue header bar beneath the button menus. The box is then selected and is coloured light green. Any homology may be double-clicked with the mouse. Upon this a text window appears giving information on the homology and on homologies of the two loci with loci from other species.

Two search facilities are provided, one for searching for an homology and one for a locus. If the text entered in either of these fields matches an homology or a locus that is present on the One-to-Many-Map, then the relevant homology box will be selected.

Button options available within the One-to-Many-Map are :

- Relative/Equal sizes - toggles between column widths equal and proportional to Map size
- Hide/Draw Chromosomes - toggles between a numeric scale on the y-axis and a banded chromosome ideogram, should this be available
- Highlight... - a menu giving various highlighting options
- Zoom in - increases the size of the graph
- Zoom out - decreases the size of the graph

Menu options available within the One-to-Many-Map are :

- Quit - destroys the One-to-Many-Map window
- Help - displays this help information
- Print - brings up the Print/Mail Selection tool
- Preserve - preserves the current One-to-Many-Map